I've been to six. My top two are almost tied, my next two basically are tied and my last two are so close it just depends on my mood.
1. Six Flags Discovery Kingdom - I always have so much fun at this park. The shows and animal exhibits are nice day-fillers and Medusa is awesome. Roar and V2 are also good coasters worth re-rides and the park has a great rafting ride. Walking around the park, you can't even tell it's owned by Six Flags (no Gotham City or DC Comics, etc.) By far the cleanest SF park I've been to and everything is just very new and fresh looking.
2. Six Flags Magic Mountain - Best coaster collection at a SF park. I love and never can get enough of X2, Goliath and Terminator. Batman is also really good, and Viper, Gold Rusher and Ninja are fun. Then, if I'm really bored of those, there's even more coasters for me to ride (only if I'm really bored though
). The park is generally improving and becoming a lot nicer (there are some beautiful areas as it is). Even though SFMM is a home park to me, every time I go I'm there from open-close. It's by far the easiest park to spend a lot of time at.
3. Six Flags Great Adventure - I'm gonna be honest, if there weren't so many coasters, this park would be below SFA/SFKK. I didn't enjoy being here much at all. The park layout is terrible, having all the rides on one side, some all the way on the other, and nothing inbetween. Ride ops are the worst I've experienced at a SF park and the place overall seems very run-down (although there were some nice areas, like Golden Kingdom and the lake).
4. Six Flags New England - I was pleasently surprised with this park. It's nice, clean, has good atmosphere and Bizarro is amazing. However, other than Bizarro everything completely sucks. I literally got my credits and just stayed at Bizarro the rest of the day. As a result, I got bored after a while... All this place needs is some more quality coasters and it could be really good. I was also surprised at how small the park was.
5. Six Flags America - It's kinda nice... but other than Joker's Jinx (which still isn't amazing by any means) nothing is worth riding. Even their Intamin tower sucks.
6. Six Flags Kentucky Kingdom - It's kinda nice... but other than Greezed Lightnin' (which still isn't amazing by any means) there is nothing worth riding. Only reason SFA is above it is because they at least (still) have an Intamin tower.