I'd definately have to say that my favorite is the Y-wing. It's the most versatile starfighter the Alliance had at it's disposal during the galactic civil war as well as one of the most versatile starfighters in the galaxy. It packs an incredible amount of firepower (standard configuration mind you), is only a little slower and less maneuverable than the X-wing, has amazingly resiliant deflector shields/hull and is extremely easy to upgrade and modify. Plus the Y-wing has an awesome looking design. 
Technically, the Z-95 was not a protoype for the X-wing but was a direct predecessor through a joint effort between Incom and Subpro. If I remember correctly, the ARC-170 (another Incom/Subpro joint venture) was commisioned after the Z-95 by quite a few years. The X-wing, on the other hand, was developed solely by Incom. Regarding the Alliance, the Y-wing was the mainstay rebel fighter before the advent of the X-wing and was also the Alliance's first hyperspace capable starfighter. The Y-wing had entered service in the Alliance about 7-8 years prior to the Battle of Yavin while the X-wing entered service about 2 years prior. The Alliance used Y-wings as multi-role craft heavily even after the advent of the X-wing, A-wing and B-wing. That's not to say that Y-wings weren't pushed into more specialized roles at all.
Guys, don't go by the technical material you get in the Star Wars games. Especially the old X-wing/TIE sims, lol. As great as they were, there was an incredible amount of inconsistancies and contradictions to the films and offical material which for whatever reason are still carrying over to present day Star Wars games. As to why these things have never been corrected... I think LucasArts considers it a non issue, which is really unfortunate and disappointing. It can get frustrating with someone who is absolutley nuts for Star Wars and wants to be able to do in the games the things we see in the films. Like myself. Plus being a perfectionist and obsessive compuslive dosn't help, lol.
Here's just one erroneous example that seems to permeate all Star Wars games (which unfortunately pertains to my personal favorite starfighter; why hamsters?!): contrary to popular belief, the Y-wing is not slow. It isn't exceptionally fast, but it actually has a pretty good top speed and is also pretty maneuverable. 
Artificial intelligence is no match for natural stupidity.