Introduction:
What to Read:
Read the tutorial and study the game's table while those first buildings build (both of these links are up at the very top of the page). The table basically explains the tech tree and what you'll need to build to unlock certain buildings and ships. Some parts of the tutorial will be over your head at the moment (all the equations for certain game actions for example) but you'll be better off for knowing where to find them in the future.
Starting Out:
Your Goal:
Your goal as a newbie is to build an outpost ship as fast as you can so you can colonize new planets. The buildings required for an outpost ship are 8 Shipyards and 8 Research Labs. The research required is 8 levels of energy, 4 levels of stellar drive, and 1 level of warp drive. Now get started.
What to Build:
First thing you should do is queue up 4 Metal Refineries. Then build a Research Lab. When you run out of energy, build whichever energy plant that gives you more energy for the least credits and when you ru n out of population build Urban Structures. Then continue with Metal Refineries and Robot Factories once you get them, building whichever gives the most benefit for the least amount of money. Now is time to build some other structures, especially Spaceports and Shipyards, which boost your economy, and also Research Labs, which cut your research time and are required to get the technology to build an outpost ship. Your economy is the most important thing in the beginning of the game, so Metal Refineries, Robot Factories, Spaceports and Shipyards are all very important.
Researches and constructions in progress do not get the benefit of new structures that are completed while they are underway. Keep that in mind when planning on when to start something - it may go faster if you wait for a construction (like a lab) to finish. It's important to keep upgrading your construction ability in line with the increasing costs of buildings.
What to Research:
Below is the order you should research in order to get an outpost ship as fast as possible. Do not worry about researching 24/7, as you will run out of credits. It is better to always be building structures and researching only when you can afford it. This way you will make more credits which will mean less time waiting until you can start your next research.
1. Computer lvl 1 (2 credits; requires lvl 1 Research Labs)
2. Computer lvl 2, (3 credits)
3. Energy lvl 1 (2 credits)
4. Energy lvl 2 (3 credits)
5. Energy lvl 3 (5 credits)
6. Energy lvl 4 (7 credits)
7. Energy lvl 5 (11 credits)
8. Energy lvl 6 (16 credits)
9. Energy lvl 7 (23 credits)
10. Energy lvl 8 (35 credits)
11. Stellar Drive lvl 1 (16 credits; requires lvl 5 Research Labs)
12. Stellar Drive lvl 2 (24 credits)
13. Stellar Drive lvl 3 (36 credits)
14. Stellar Drive lvl 4 (54 credits)
15. Warp Drive lvl 1 (64 credits, requires lvl 8 Research Labs)
Also remember to love that damn table. That table is your bible after this guide. The link is always up at the top of the game interface.
Building New Bases:
Scouting:
Once you get Warp Drive you may be tempted to build an outpost ship right away, that is fine. Now just where are you going to send that outpost ship? What, you don't know? Thats where scouts come in. Scouts, with their superior speed, enable you to find a suitable planet to send your outpost ship to. The most effective way to scout is to move your scout to a corner of a neighboring region, just over the edge. You do this so that you have the shortest possible travel time between the four regions and you can hop from across the corner and see all 4 regions in short order. Check every system for good planets (see below for what defines a good planet), bookmarking and labeling the ones you find before moving on. You move a ship by first going to the destination region (from the Fleets screen by clicking on a region adjacent to yours), then picking the system and planet (It has to be an asteroid or a planet, no gas giants or asteroid belts),you want to land on (remember, a corner). Copy the address, then go back to your home planet and click on the fleet there. Select one scout by putting 1 in the box next to scouts. Put the copied address up top, then click move. Now you just have to wait.
Deciding on a Base:
So now you have your scout on its way, or maybe you are doing it the slow way and having your outpost ship search for a suitable planet, but either way, you need to know what to look for.

General:
The most important parts of choosing a new planet center around Fertility, Metal, Energy, Area and Moons vs. Planets vs. Asteroids.
* Metal is very important to choosing a planet as it decides how quickly you can build and also how high your economy can go. Never take a 1 metal planet, and 3 metal planets are usually superior to 2 metal planets. Production planets need to be 3 metal, econ and research planets benefit from 3 metal, but it is not necessary.

* Energy is an important resource for you to consider, and getting a planet with 3 or 4 solar or gas will make energy much cheaper both in the short run and in the long run. High energy is most important for Production planets, but also is important for Jump Gate planets and planets you intend to defend extra well. Energy should not be chosen over metal.
* Fertility is important as it affects your population capacity. Low fertility can be harmful early in the game, but you can fix it later with Biosphere Modifications later so it becomes less important. Lots of times fertility comes at the expense of energy, and the two are more or less equal in importance.
* Area is something to think about mostly for Production and Research bases. Asteroids have low area and are not very good as either. Planets of course have the highest area, but there are drawbacks to planets. Overall, area is less important than the above 3 characteristics.
* Moons vs. Planets vs. Asteroids comes down to the prices of some structures which are 50% off on Moons and 75% off on Asteroids. These structures are Biosphere Modifications, P-Rings and P-Shields. If you have low fertility, having cheap bio-sphere modifications can be important, so moons and asteroids give some benefit there. If you plan on defending your base extremely well, cheap P-Rings and P-Shields are very important, making moons and asteroids much better than planets. At 10 P-Rings, Planets are better for their increased area, but at 15 P-Rings, Moons become better for discounts on Rings. It comes down to how much defense you want. All in all, choosing a moon vs a planet is the least important choice in colonizing.
* One other important thing is that you don't want your bases too close.
* It is a very bad idea to have more than one base in the same system, and a bad idea to have multiple bases even the same region.
* Having your bases distanced from one another gives you better scanners and scouting in the galaxy, and makes it harder for one large fleet to conquer you.
* So do not build two planets in the same system, and unless you cannot help it, do not build two bases in the same region.
Economy Bases:
Your economy is very important, and likewise your 2nd base should probably be an asteroid as they are very cheap to get up to a nice economy. The best asteroids are 2nd position asteroids, followed by 1st position and 3rd position asteroids (1st vs. 3rd position asteroids is a topic of much debate over which is better, but both are good choices). Without having a scout in a region the game still reveals where asteroids are (albeit you can't see whether they're taken or not until you have a ship in the region). So go out and find a good asteroid and build a base there, and after defenses and construction, concentrate on building economy boosting structures. Your 3rd and even 4th base can be asteroids, so keep those scouts looking. Crystals can achieve higher economy than asteroids, but have 2 metal so they have lower construction and production, but many people choose crystals over asteroids, and if you can find crystals, having one or two does not hurt.
Production Bases:
Your 4th or 5th base should probably be a production base. You want 3 metal for your production planet, along with plenty of area and energy. The best production bases are rockies, followed by metallics and craters. For production bases 2nd position is best, with 1st position being second best (A lot of energy is required on a production base) and then 3rd position (The most important stats for a production base to have are 3 metal followed by high energy and high fertility). Production bases are considered the most important bases in AE, as they provide good econ, produce ships quickly, and can even be used for research bases if one so wishes.
Research Bases:
After a production planet your next base should be a research base. There are many different options for research bases, and choosing one depends on ones preference for construction and production. You can choose the same type of planet as you did for a production base, rocky, metallic or craters, and you will have the benefits of 3 metal, higher econ, and higher construction and production. Or you can choose a 2 metal planet (Gaias are the best, followed by Earthlys and then Arids) which will usually have more area, more fertility, and often times more energy. Area and fertility are more important for research planets than other bases, as you are building 20 or more labs on these bases, and that takes up a lot of space and population. Energy is not as important for research bases, and a planet with 2 metal can still achieve high construction, production and econ. It all comes down to what you find and what you prefer.
Order of Building:
Everyone has a different style with building an empire, but a good guideline is to start with econ bases (2 or 3), then build a production and a research base, and then build based off of what you find to build on and what you need. If your research is lagging, get a new research base, and the same with econ and production. My suggestion is to not pass of up a good rocky or a good asteroid just because you are looking for something else, they are hard to find and you should take them when you find them.
Base Defenses:
Under Protection (Your First 7 Days):
Build a single fighter as soon as you can to protect your trade routes (otherwise they can be pirated). By the time protection is up (7 days) you should have at least 100 fighters (no other units are needed really) over your base and 2 sets of Missile Turrets minimum (a set of Ion Turrets should follow very shortly), and you should be researching towards stronger turrets constantly. No more than 2 different sets of turrets are required on any base, so you will disband your missile turrets once you get Photons and Disruptors. (Weak turrets take up space, energy and population and do not do much damage later on in the game).
After that:
Two sets of Ion Turrets is recommended, and after that Photons and then Disruptors should follow shortly, all the while you need to be researching the tech required for P-Rings. Fighters should be constantly increased, as they increase the cost of someone taking your base. Try for around 1000 fighters when you have Photon Turrets, and 2000 fighters when you have Disruptor Turrets. A single set of Deflection Shields can help a lot early in the game by increasing the amount of fleet players have to bring to take your base.
P-Rings:
P-Rings are the best and most expensive defense in the game. A single set early in the game will almost guarantee the safety of your base. As the game progresses, a second set becomes required and depending on the economy and designation of the base and the galaxy you are in, a third and forth can be necessary. A single Planetary Shield can be helpful by increasing the amount of fleet enemies have to bring to take your base.
Fortresses:
Special defenses are required for the bases where you might want to keep your attacking fleet while you sleep. These bases are referred to as "Fortresses". A good fortress has lots of P-Rings, lots of P-Shields, some Disruptor Turrets, Ion Turrets and a lot of Fighters.
* P-Rings are the most effective way to prevent your base from being taken. P-Shields can help keep your P-Rings alive if you have enough fleet to require the enemy to attack more than once. Disruptor Turrets become useful once you have so many P-Rings that they become too expensive. Ion Turrets are the only weaker turret worth keeping later in the game, and are even worth building lots of on your Fortress bases. They soak of fighter damage, making it more expensive for an enemy to fighter drop your fleet. (This only really pays off if you plan on having a lot of fleet on your base, which you will on your fortress).
* Fortresses also have to have at least 13 Command Centers. 13 CCs is the magic number because is makes your Fighters able to hit Heavy Cruisers (under 13 and someone can use just Heavy Cruisers against a base with too many fighters and make a good profit). 20 CCs is a good number to aim for on a base where you plan to keep your main fleet. 15 P-Rings, 10 P-Shields, and 20 Ion Turrets is usually considered the minimum for Fortresses.
* A base with the above defenses can still be a target for the enemy depending on what fleet you are keeping over it. If you have a Death Star and a bunch of Carriers and Recyclers, kiss your base goodbye. All fleet over your Fortress needs to be balanced by Fighters and lots of them. If you have a Leviathan (200k worth of fleet), plan to have 40,000 Fighters sitting with it (20k worth of fleet). Fighters are the most useful unit in the game for attackers, and using 100,000 to take out a base is rarely a smart move. By balancing units that can be attacking for profit with fighters, you are making the cost in fighters too high for a smart player. Build fighters on your other bases and ship them to your fortress, having a huge stack of fighters on your fortress is very good at preventing attacks and for replenishing your mobile fleet.
End Game Defense:
When you get P-Rings, the entire shape of base defense changes. So follow these simple steps.
* Step One: Build up P-Rings (see above)
* Step Two: Add a single Dreadnought as base defense (This stops your trade routes from being easily pirated). Two Dreadnoughts for those who are extra paranoid.
* Step Three: Remove your fighters. With high Armor tech, keeping fighters over your non-fortress bases is just making it more profitable for the enemy to attack. (Debris depends on level of armor)
* Step Four: Disband any CC's outside of your Fortress Base. They are just wasting space that can be used for more useful structures.
Hint: A base with 4+ sets of P-Rings and 1-2 Dreadnoughts is the best defense in the game.