In addition to appearing on several studio albums with Fates Warning, Moore has appeared on compilation discs and also performed as a guest musician on releases by a variety of bands. In 1998, he teamed up with Steve Tushar for a cover of Metallica's "The Thing That Should Not Be" that appeared on a tribute disc called The Blackest Album, and the same year the duo contributed two tracks to a video-game compilation disc called Sonic Adventure Remix. Moore was also a guest musician on Tushar's Carbon 12 album in 1999, as well as his Oscillate album in 2008.
More recently, Moore has contributed production, vocals or keyboard parts to music created by a number of his fans who contacted him by e-mail. In 2012, he appeared on one track of Italian bassist and composer Alberto Rigoni's Three Wise Monkeys album as well as several tracks on U.S.-based experimental rock band In Progress's North Atlantic Echoes EP. He also contributed to a track on Italy-based progressive psychedelic rock band Chaos Venture's Chaos Venture 1.0 album in 2013, and to an album by Beirut-based progressive rock musician Amadeus Awad in 2014.