(Edit : Sorry if there are mistakes, English isn't my native language)
My two cents : I think each Paper Mario game has its own qualities and flaws, so they are all worth to play.
In my opinion, Color Splash and Paper Mario 64 are the best entries in the series. They are very charming, have a good level-design (especially Color Splash), nice combat system, good soundtrack (especially Color Splash), and each place in these games has its own little and charming story or original idea (some of these ideas are really genius).
Super Paper Mario is also very good, with a nice side-scroller Action-RPG gameplay, the 2D/3D gameplay idea (although it's a little too underused), the best story in entire Mario series (even better than each Mario & Luigi's story, it's also the darker and saddest story in the series), the best side-quests (the two pits with 100 levels of fights are incredible trials). This game has problems (some levels are really too empty or repetitive in their level-design), but it has a strong personality.
Paper Mario Sticker Star is nice, because this game has a good level-design, good puzzles (except for the "things" which are too tedious to use, it was largely improved in Color Splash), very good soundtrack, good 3D graphics. It's biggest flaw is that it's background is too light, there is no story, no character (except the Wiggler who is nice), no narrative (except the Snifit TV game and the incredible haunted mansion level).
About Paper Mario Thousand Year Door, I think this game is nice, but totally overestimated. It is very good to play it for the first time, but its replay value is horrible : too much back-tracking, the worst level-design in the entire series (it was terrible for me to play it again just after Color Splash and even just after Paper Mario 64).
I'm always very surprised that many people complain about Super Paper Mario's flaws (some empty levels, repetitive and uninteresting tasks, or some levels without gameplay) but are so indulgent with Paper Mario TYD that has exactly the same flaws than SPM's. It's even worse in TYD, because I think these flaws are harder to bear in an RPG with turn-based (and often unavoidable) combats (it's tedious in chapter 4 and 5 with a lot of back-tracking, or the horrible chapter 7 with the white general Bob-Omb) than in a side-scroller Action-RPG like Super Paper Mario. I think people should replay TYD : they'll have a bad surprise, after all the other Paper Mario games offered to us. I was very surprised to realize that I had more fun replaying Super Paper Mario than replaying Paper Mario TYD.
Now, you can throw stones at me. ^^