For me, it really depends on the song, but because STP is so fantastic as a live band when they're in the groove, it presents an interesting question.
For instance, there's an acoustic version of Sour Girl out there, with just Scott singing and Dean on guitar, with no Robert and Eric. I actually like this version better than the studio No. 4 version. You can really hear how brilliant yet simple the melodies to the song are without all the overtracking and supplemental instruments heard in the studio. Same thing with Wonderful, off Shangri-La Dee Da. There's an acoustic version on the Family Values 2001 Tour album that's a little more stripped down than the album version, but beautiful.
The live version of Coma from Rolling Rock 2001 is pretty explosive, as is Long Way Home, also from that same show.
Sex & Violence, off No. 4, is another example. Check the live version of that from the Thank You DVD - absolutely balls-to-the-wall.
Some studio versions that I actually prefer include Big Bang Baby, Days of the Week, Creep and Plush (oddly enough).