Ok, here are my tips and tricks. I will only stress point not already covered by others here (ok, that’s no strict rule

).
AI_ANGER.TXT
This is an important file for the AI diplomacy. Don’t give the Ai to much anger points in a single row. There are many ways to anger the Ai but few to make them friendly so beware if you don’t want to create psycho races (and there are already many out there).
AI_CONSTRUCTION_FACILITIES.TXT
A very important file. Make sure you build all your special buildings your advanced trait gave you but watch out for buildings does not use. A good example for this IMHO are the training facilities: The Ai will actually use them (i.e. place a ship/fleet of them) BUT as the AI tends to be busy sending all its ships and fleets from one end of the galaxy to the next the AI will seldom use this facilities. On the other hand they will use up valuable building slots so weight if their use of space is really worth it (IMHO: no). Sorry, Tampa.

Try to only use a small amount of different colony types. The AI is limited in the ways it can choose these colonies. By creating dozens of different colony types you will loose your focus and you can’t make sure the AI actually build the right colony with the right facility at the right place (e.g. a military installation in every system). A good example of a unneeded colony type is the “construction colony”. You need lots of space yards and therefore should integrate them in nearly all colony types with a certain size.
On a side note, make sure the AI researches all important buildings fast at at least level one. This way the Ai will follow your build plan and will upgrade the facilities in time. If you do not research these facilities in time the AI will have used up all the slots with the buildings from the “catch all” line.
AI_CONSTRUCTION_VEHICLES.TXT
There is one confirmed and known bug with recon satellites: These satellites will not be counted toward the production total once they are launched in space. If you call them, the AI will build them until the “units in space limit” is reached AND all the cargo on all planets is used up. Need I say that this will take forever and that no production “below” the recon satellite call will be executed?
You can circumvent the problem somewhat by making “combat” satellites recon satellites. “Combat” satellites are counted correctly. This will prevent your race from using combat satellites, however…
Make sure you build some Space Yard Ships. If the are not constructing something, there are actually used as repair ships and will go after your crippled zero-movement ships. But beware: The AI will only consider a ship a SPS if there is a space yard on board. You can give it some repair bays to, but there must be a space yard to be a SYS.
AI_DESIGNCREATION.TXT
Make sure you call each item as specifically as possible. For example:
To add organic armor to a design you could use the “Armor Spaces Per One” line or you could use the“Misc Ability 1 Name:= Armor”. Both ways will result in organic armor being added IF
a) you have organic armor at all
b) there is no “better” armor.
Unfortunately, the AI considers any armor of level 4 or higher (e.g. emissive, stealth and scatter armor) to be “better” armor.
Therefore, the best method to call an item is by a unique ability of this item. For organic armor, this is regeneration. So, the best line would be “Misc Ability 1 Name:= Armor Regeneration”. Now the AI will always use organic armor.
AI_PLANET_TYPES.TXT
Like Tampa said, this may be the single most important file for your race. If this is not done properly your whole race will fall apart as they have no economy to sustain their fleet.
AI_POLITICS.TXT
The “Military Alliance” should be the highest treaty your race should make. Not only will your race get angry over allied colonized planets (you can turn this one off) but much worse: The AI will gain star maps and then sent colonizers to colonize these nice huge correct atmosphere planets 500 LIGHTYEARS AWAY WITH A TRAVEL TIME OF ROUND-ABOUT 50 TURNS!
So, NEVER EVER LET YOUR AI MAKE A PARTNERSHIP-TREATY, NEVER EVER MAKE IT AN ANCIENT RACE!
Puh, enough screaming. But this had to be said.
AI_STRATEGIES.TXT
Listen to Tampa, he knows what he is doing.
.EMP FILE
Make sure the line “Ships should not move through minefields” is OFF. If not, all your ships will not move through mines INCLUDING your minesweepers. It is a known bug and MM is working on this one.
GENERAL
Two Last things that are bugs and will effect how you design your race:
1.) Boarding ships will not actively engage an enemy ship even when armed with a "real" weapon like a depleted uranium cannon. The boarding ship (BS) will run for the battle field corner until any of the enemy ships lose all of its shields. If enemy shields are down, the BS will board the enemy.
2.) The Ai is not always creating a new ship design if certain techs become available in simultaneous games. If sensors, combat sensors or shields are researched, the AI should initiate a new design but it does not. It will only add these components if the next bigger ship class is available (the AI then starts a new design process and adds every called for available tech). It has no problems to upgrade the ship designs if only a newer component is researched (i.e. shields I are in the design and shields II become available).