Oh man, this was a tough choice. I decided I could only vote between those I own: Star Wars, Wheel of Time, D20 Modern, and Traveller (or T20)...
The quality of the first three appealed to my effeorts to acquire good material for the $$. Nearly flawless. None of them have disappointed me...
However, the first Sci-Fi RPG I got involved with was Traveller. It has a long, and sometimes rocky history, in the gaming world, but I always loved the setting!

Now that I have a d20 version of it incorporating many elements of my Classic Traveller library that I liked. While not as nearly flawless as the other 3, it remains my favourite--my totally subjective choice
Which begs a question: does favourite necessarily mean the game is perfect in terms of mechanics, editting, and other issues of quality of product? Not for me--a good game has good ideas, is original, and captures my imagination, in spite perhaps being a little "rough around the edges"! (Of course sometimes a good idea can be spoiled by bad execution. But mild imperfections do not trouble me

)
-W.