If I'm playing as the University (and I like playing as the University, oh my, yes), and I'm playing SMAC (because it took me years to finally buy the add-on, which I still haven't played very much), then I have to recommend the following projects:
1) Hunter-Seeker Algorithm - negates one of your key weaknesses, and lets you do more research, lovely lovely research!
2) Virtual World - I always love free stuff, and this helps you with your drone problem. It's almost as if it was... designed for them...
3) Human Genome Project - Again, the drone problem is lessened to a degree, and early on, too. I tend to take later projects as they come.
4) Citizen's Defense Force - I'm a bit of a pacifist, and I don't like sending out huge invading forces, so I need something to defend myself, and plays to my love of free stuff. I like the idea of mad scientists defending themselves in ridiculously-well-protected bases, too. Probably with lasers.
5) The Living Refinery - The fifth one is a tricky choice, but I usually kick myself if a computer gets this before I do, perhaps moreso than (4). By the point this comes available, one or other of the 'nasty' powers (Believers, Hive, Spartans) has usually risen to prominence and is knocking on my door asking for a cup of retrovirus. I usually say 'nyet', but need to support my military somehow, despite my focus on (occasionally evil) science. Hence this.
Others of note might be The Network Backbone and The Weather Paradigm. Pure SCIENCE ones are nice, too, but I can let one or two of these go without wanting to kick the computer in the network node.