Rogue Squadrion II: Rebel Leader on the Gamecube was my absolute favorite.
A close second is the original Rogue Squadron on the PC.
Third is the Star Wars Arcade game with the vector graphics - but only if played on the actual arcade game with the real controller. Using MAME with a mouse just isn't the same.
Fourth is Battlefront on the PC (didn't like Battlefront 2 that much)
Fifth is Rogue Squadron III on the Gamecube. Just never got into it as much as Rogue Squadron II. I am currently replaying Rogue Squadron II and it is still very fun and challenging.