Of the ones I've been to (missing Over Georgia, Mexico and Frontier City so far), I'd put them into the following categories - based on my experiences and days at those parks.
Six Flags America - dump.
Six Flags Darien Lake - see above, but at least I got the Superman cred at this one.
Six Flags St. Louis - the park itself isn't bad, but it's not exactly great either.
Six Flags Discovery Kingdom - I went pre-RMC, and didn't think the place was up to much.
Great Escape - pretty, but the coaster selection is crap. [I'd hazard a guess that Frontier City would slot in here somewhere]
La Ronde - bottom of the mid-tier, but I really enjoyed my day here and I quite liked the inner-city-but-not-really vibe it had going on.
Six Flags New England - I went pre-RMC, but still thought this had a pretty decent coaster selection.
Six Flags Fiesta Texas - a decent park marred by a rather heavy handed bad weather policy.
Six Flags Great America - top of the mid-tier, but I also only went pre-RMC (and Maxx Force) so it might jump up a tier if I were to revisit. [I'd hazard a guess that Mexico would slot in here somewhere]
Six Flags Over Texas - actually had a really great day at this park.
Six Flags Great Adventure - a pretty solid line up, and home to a few of the true icons (albeit none of them are 'stunning').
Six Flags Magic Mountain - best of the lot, in my opinion. [I'd hazard a guess that Over Georgia would slot in here somewhere]
Can't decide between Magic Mountain and Great Adventure for the top slot. MM was my first taste of the Six Flags experience and I enjoyed it immensely. X2 is still a top 5 coaster for me.
On the other hand Great Adventure, despite having fewer coasters, seemed like a greener, nicer place to be.
Great America sits firmly in the middle. Lots of coasters, some very good, but none of them particularly stand out for me and it's also a bit... what's the word? Tarmac-y.
At the bottom we have Discovery Kingdom and St Louis. Neither of which are actually bad per se, just somewhat forgettable.
Of the ones I haven't been to, I'm quite keen to get to Over Georgia one day, and at least one of the Texas parks looks good but I can never remember which one.
Over the years, I've been to MM on 5 different trips (took me 3 trips to even get X/X2, stupid thing), GAdv on 3 different trips, GAm on 3 trips, STL on 3 trips - but MM was also my first experience of a 6F park (first experience of a US-chain park in fact). (The other ones, just once or twice apart from Mexico)
There's some very good coasters at GAdv no doubt, but the park itself I borderline hate, awful layout, shabby and last time I went whole sections closed off, whereas I've always had a pretty good time at the Mountain (even back in 2010 when I had food poisoning the whole day). GAm I quite like too but STL I only went to by accident the last time.
I can never decide whether I like Six Flags Great Adventure or Six Flags Great America best so they're joint top. SFGAdv has some bit hitters like Ka, Toro and Nitro but SFGAm has an interesting, varied line-up of cool, quirky and fun things like whizzer, the log flume, goliath, american eagle etc. Six Flags New England- I feel like this park lacked the atmosphere of SFGAdv and SFGAm. It's got some good stuff but not loads of amazing stuff. Six Flags America - a few interesting things, like superman and joker's jinx but lacking a bit. Six Flags Darien Lake - simiar to SFA but lacking a bit more.