There's long been an argument that Coma and Wonderful would have been better choices for SLDD's singles than Days of the Week and Hollywood Bitch, and I think those songs may have done better in 2001... But since Down and Sour Girl hardly get radio play these days, I don't think anything they released off of No. 4 or SLDD would have the lasting power of their first to albums.
I think that has more to do with how much the music landscape changed in the late0-90s than anything to actually do with the band. I hardly hear anything on the radio that bands like PJ, AiC, and Soundgarden released after '96. I think bands like STP are just pigeonholed into the early 90s unfortunately.
I think the songs that would stand the best shot at being played today would be off of Core and Purple. Sin, maybe, and Piece of Pie. Hell, Dead and Bloated was never released as a single but that gets radio play, so that's an obvious one. I think Silvergun Superman could have been a pretty big hit, and maybe even Kitchenware and Candybars... It has the perfect "quiet/loud" sound for that era, and is a nice moody ballad.
I don't know if anything off of TM besides Trippin' would have any staying power. Trippin's the only real hard rock song, and it's about the only one that really gets radio play. Maybe Seven Caged Tigers could have worked, since it has a heavy Zepp feel and is less poppy than most of the album.
As for the newer albums. I've always though Take A Load off should have been the lead single off of Peace, but obviously Scott's inability to sing it live would shot that down.
As for Butterfly, I think Roll Me Under (and maybe the album) would have done better if it were the lead single... Then maybe Thought She'd Be Mine as the second single for a crossover hit, and then finally Meadow as third single. But that's just speculation.