Not super qualified to comment as I only have Syncestra, Ocean Machine, Ziltoid, and The New Black. I heard City around when it came out, but I was not really ready for SYL at that point in my life. I didn't get it. Weird to think back on that now.
Anyhow, his general wackiness combined with his musical talent and his prolificness makes me think of Frank Zappa a bit.
I actually think the Townsend/Zappa comparisons make alot of sense. There's alot of similarities between the two. The only other artist I can think of that can pull off a silly comical concept like Ziltoid would be Frank Zappa. Not to mention that they both had a knack for layering.