Sarah and I have finished playing through the games "Paper Mario", "Paper Mario: The Thousand-Year Door", and "Super Paper Mario" last week (including the various Pits of 100 Trials). We played them all on the Wii, because even though Super Paper Mario was the only one released explicitly for that platform, Wii maintains compatibility with Game Cube games such as Thousand-Year Door and Paper Mario although originally released for the Nintendo 64 is now available as a pay for download game on the Wii's Virtual Console. So, yay for Nintendo!
I think my favorite of the three is Thousand-Year Door mostly because of the RPG attack system. In Thousand-Year Door and Paper Mario when you come into contact with an enemy you go into an RPG style attack system where you take turns selecting actions. In Super Paper Mario you still have hit points and such, but you don't go into a turn based RPG style attack system, rather you do the regular Mario jumping on bad guys thing (or hitting them with a mallet etc...). Thousand-Year Door and Paper Mario are very similar in terms of game play but Thousand-Year Door looks very pretty and has made improvements to how your party-mates are handled in battle (they have HP and can fall as you would expect) and there's an audience that cheers you on during your battles.
Even if the gameplay sucked the humor throughout the series might be tempting enough. Mario's clothing and mustache are mocked throughout and standard RPG expectations are subverted. I hate to describe any of these moments for fear of ruining anything but, for instance, an optional and very difficult enemy who may only be killed after hours of work only results in one experience point, or a very intimidating enemy who you imagine you'll have to fight actually challenges you to a quiz.
Despite how I personally rank them, all the games are great and I'd recommend any of them.