My all time favorite game and game system is the long out of print Top Secret/S.I. from TSR. I think it is one of the smoothest percentile based systems I've seen and I think it deserves a retro-clone treatment, like OSRIC or Four Colors (4C) (stripping the system out of the setting and using it as a generic gaming system for most types of games). The biggest mark against TS/S.I. is that the fan base is almost non-existent. There are many out there who love the game, but the number of people who still play and support it is shrinking. That holds a lot of weight for me.
The next game system I can't choose between is Savage Worlds. I have never actually played it, though I've read the rules many times and I really like the concepts- using die types for ability levels (d4 is low as d12 is very good). I even have a few of the campaign setting books. All of the Savage World products are incredibly well made. A good thing for Savage Worlds is that it has a fierce fan base. There are tons of resources to draw from for the system. One thing going against it is how married the system is to tactics and battle maps. My comfort is to rely on this aspect as little as possible. I've always been more about story than about the mechanics of combat. A good alternative for Savage Worlds may be the Cortex system that runs Serenity and Battlestar Galactica RPGs. Cortex is also die types for ability level, but appears to be more geared towards story than tactics.
The last system is True20. This one was a pretty good attempt to take 3rd edition Dungeons & Dragons (d20) and strip away a lot of the battle mat tactics out and have a near compatible d20 system. True20 is far easier than D&D and probably moves along much faster, as well. The fan base for True20 is out there, though I don't think it is as big as Savage Worlds. I even tried my had at contributing by starting the unofficial True20 Wiki page.