I am by far too indecisive to name a few Projects I like more, but I shall attempt to create a small list of favourites. Now of course in truth these vary depending on just which faction I play with, and on how well the game goes. If I am leading by far I will always try to build all the projects I can before the AI does, but that is hardly always a possibility.
Now I'll make a "top five" here. In no special order mind you, just ten Projects I like very much.
1. Weather Paradigm ( despite knowing full and well that having a few extra formers well makes up for the bonus WP gives I still like it. It's a fairly useful long-term project, especially when building those time-demanding Boreholes )
2. Cyborg Factory ( needless to say it is useful for *any* faction to receive that lovely all around +2 bonus to morale, one does not even need be militaristicly aligned to see the benefit of having superiorly trained troops )
3. Cloning Vats ( super-sized cities in no-time, not only does it remove the bad parts from Thought Control, but it also makes the cities grow enormous in the blink of an eye. Kind of kills the usefulness of the Plantery Transit System for one )
4. Hunter-Seeker Algorithm ( whilst probes of your own may block out enemy ones, I find it so much more comfortable to be positively IMMUNE to probe operations rather than just being protected from them. Not only is it annoying to rebuild lost probes but they don't quite work to defend your entire armed forces either )
5. Citizen's Defence Force ( admittedly building and keeping Perimiter Defences up is not much of a hassle, but for much the same reason as the HS I like CDF. With it you will never be without defenses, and that is nice. The silly AI can't sabotage it and you don't have to worry about building it )
There's a list for ya. Of course, like I said, I like them ALL! But I tend more towards "global" projects than I do such ones as Merchant's Exchange, Supercollider etc, because I do not like ones only affecting one base ( if globally in the big picture )