Nelson formed Harvey Danger in 1993 and played with the band through to its farewell show in 2009. In addition to being the band's lead singer, he was also its Songwriter and keyboardist. The band's debut album Where Have All the Merrymakers Gone? was released in 1997 and was certified Gold by the RIAA for sales of 500,000 copies. The album contained the hit single "Flagpole Sitta", which was featured in the 1999 film American Pie and was later used as the theme song for the British sitcom Peep Show.
In 2001, Nelson formed a second band, The Long Winters, with John Roderick. He left the band in 2004, and Roderick has continued the group as a largely solo effort.
In 2006, Nelson published his first book, an entry in the 33⅓ series on Joni Mitchell's Court and Spark. His essay "Dead Man Talking" was published in the Da Capo anthology Best Music Writing 2008.
In 2008, Nelson co-wrote and played a supporting role in Humpday Director Lynn Shelton's third feature film My Effortless Brilliance, which enjoyed a successful run on the film festival circuit and was released on DVD by IFC Films in November 2009. He has also acted in David Russo's cult film festival hit The Immaculate Conception of Little Dizzle and alongside Dax Shepard in Kathryn Aselton's The Freebie, which was released in September 2010.
On June 4, 2013, Nelson released his first official batch of recordings to bear his name, Make Good Choices, which includes contributions from Chris Walla (Death Cab for Cutie), Peter Buck (R.E.M./Minus 5), Matt Pence & Scott Danbom (Centro-Matic), Howard Draper (Shearwater), Dave Depper (Loch Lomond, Fruit Bats), Rachel Blumberg (The Decemberists/M. Ward), Adam Selzer (Norfolk & Western), Steve Fisk (player: Pell Mell, Pigeonhed; producer: Nirvana, Beat Happening, Unwound), and others. Sessions arose over the course of several years between Nelson and his collaborators' other projects.
