(an incomplete list)
Note: I've excluded the countless college a cappella groups I've seen. Also: many of these acts were opening acts or double-billed acts who I didn't actually want to see. I'm looking at you, Wallflowers.
Barenaked Ladies Blake Babies the Bobs Body Count Butthole Surfers Cake Jonathan Coulton the Charms the Church the Connells Crash Test Dummies Crush dada Da Vinci's Notebook Damn Personals Kris Delmhorst Mike Doughty Everclear Fastball Five O'Clock Shadow Flaming Testicles of God Fountains of Wayne Freezepop Great Big Sea Guster John Wesley Harding Juliana Hatfield Honest Bob & the Factory-to-Dealer Incentives House Jacks Jane's Addiction Jesus Jones Jim's Big Ego Ben Lee the Lemonheads Lifestyle Lush Marcy Playground Ashley MacIsaac Pamela Means Paul Melançon MC Frontalot MC Lars MC What I Mean Meg and Dia Men At Work Mighty Mighty Bosstones Mission of Burma MSG Peter Mulvey Nine Inch Nails OK Go Paul & Storm Phish the Pixies the Pontoons Primus Henry Rollins Band Rush Sheila Divine Siouxsie & the Banshees Soho Soul Asylum Soul Coughing Spin Doctors Sugar High Diaries Superhoney They Might Be Giants the Wallflowers Walt Mink Weird Al Yankovic YTCracker