Super Paper Mario is my favourite Paper Mario but I feel that Paper Mario: The Thousand Year Door is the best RPG of the lot (though I haven't played the SNES Mario RPG or whatever-it-is-called...but it's not a Paper Mario game). 

How about you?

TTYD was really good, but I've never played the original.

My favorite is easily the first Paper Mario game, The Thousand Year Door was good just not as good as the original and Super Paper Mario was also good but kinda pissed me off because i really wanted another Paper Mario RPG not a platformer.

Super Paper Mario.

1A.Paper Mario
1B. TTYD
2.Super Paper Mario

I only have played Paper Mario and Super Paper Mario, and the first game is my favorite of the two. Although, I really rather enjoyed SPM more than i thought i was going to. I thought it was a great game, just not as good as the original.

Super Paper Mario was trash in my opinion, and the original was the best.