Hell 'O' Death Day: The name Key and Ogre used when they opened for Chris & Cosey on their 1985 Canadian tour. Some of this material later appeared on editions of Skinny Puppy's Remission and Bites. 
Hilt: Begun in the mid-1980s by Key and Alan Nelson as The Flu, who self-released some of their early material on cassette. Listed below are Hilt's releases.
Mutual Mortuary: A one-off project of Ogre and Bill Leeb. "Shadow Gods" and "Hateless Insanity" were released on Belgian cassette compilations, without Ogre's consent. 
Ogre and Rave: Ogre and Dave "Rave" Ogilvie had several small side projects. "Aftermath" never released anything, while "Raw Dog" included contributions from Dave's wife Rosie. . The track "Ode to Groovy", while credited to Skinny Puppy on an animal rights benefit compilation,  was actually just Ogre and Rave. 
ohGr: Ogre's project with Mark Walk, originally known as "W.E.L.T.". Their first album was originally recorded in 1995, but was held up in legal issues with the label. An early incarnation of W.E.L.T. included Ogre and Al Jourgensen, whose unreleased track "Noreen" evolved into Ministry's "The Fall". Ogre and Mark Walk have also recorded as "Ogre & Mark Walk". 
PTP: Ogre contributed vocals to the song "Show Me Your Spine" by this Ministry side project, which was used in the 1987 film RoboCop, but was not commercially released until 2004 on Ministry's Side Trax compilation. 
Raw Dog: a collaboration between Ogre and David "Rave" Ogilvie. Contributed the track "Raw Dog" to the 1993 compilation Rivet Head Culture on the record label If It Moves.
Notable guest appearances of Skinny Puppy members with other bands include:
Ogre with KMFDM: Ogre performed vocals on "Torture" from KMFDM's Symbols, and joined the band for its 1997 tour. He also performed vocals on "That's All" and "Full Worm Garden" on KMFDM's Adios (1999). 
Ogre with Ministry: Ogre toured with Ministry in the late 1980s and co-wrote "Thieves" and "Breathe" on Ministry's The Mind is a Terrible Thing to Taste (1989). Ministry would often perform a live cover of Skinny Puppy's "Smothered Hope" during this period. 
Ogre with Pigface: Ogre toured extensively with the industrial rock supergroup Pigface in the early 1990s, and appeared on a number of their recordings and videos, including a cover of Skinny Puppy's "T.F.W.O.". 
Ogre with Revolting Cocks: Ogre appeared on several early Revolting Cocks tracks and videos. 
Key and Goettel are listed as "additional personnel" on Decree's 1996 album Wake of Devastation, a variation of that album's "Talons Grasp" appeared as the Skinny Puppy track "Those Loud Neighbours" on Back and Forth Series 7.
Goettel played keyboards on "Night Returning" on Sister Machine Gun's debut album Sins of the Flesh (1992).