The Thousand Year Door, for graphics, story and partner system. SPM was quite a radical departure from the usual PM gameplay, so it can't really be called my fave.
I'm with the crowd on Paper Mario The Thousand Year Door. While Paper Mario excels better in some categories, I think PM:TTYD excelled better and overall.
PM:TTYOD is my favorite even if The Crystal King is not in the game. It was everything that was great about the firs one just better greater. And I liked the partners better in this one too.