This is another one with a lot of potential answers. My list of Science Fiction RPG's in chronological order of when I started playing them, looks like this:
- Star Frontiers
- Gamma World (2E)
- Star Trek (FASA)
- Space Opera
- Twilight 2000
- Gamma World (3E)
- Star Wars (d6)
- Mega Traveller
...and that just gets us to about 1990.
I thought about going with what I've played most recently but the SF games have been pretty sparse around here. I did just run the Apprentices through the Age of Rebellion Beginner Game but I'm not going to declare it my favorite just yet! The last SF type thing I ran was Star Wars Saga Edition a year or two back and while I do like the game a lot I'm not really ready to declare it my favorite either after letting it sit for 18 months.
Sometimes I get a Star Trek thing for a few weeks, sometimes I get a post-apocalyptic thing, but nothing really dominates long term in RPG's. The longest-term interest I've had is Traveller, and the current Mongoose Traveller incarnation is great, but I haven't run a Traveller game in years.
I'd say the position of "Favorite SF RPG" is ... open.
If we expand it a bit to "Favorite SF Tabletop Game" then it gets very easy:
Warhammer 40,000 has been a steady presence in my hobby life for more than 25 years now. I don't care as much for the RPG's but it is a major player in miniatures, board games, and computer games for me and now for the Apprentices too.
Second place here would probably be the Battletech universe of games, followed by Star Wars and Star Trek, but at this point we're way past considering RPG's only.
So there's my complicated answer to what seems like a simple question.