Oh don't let me get started, as I got like 5 pages of them in my anime list...
Seriously though, probably the biggest fanon ship I sail in the cartoon world would be Spiderman and Black Cat in the 90's cartoon series. Felicia >>>>>> Mary Jane in that universe.
In another Spiderman universe (Spectacular), of course I support GwenXPeter. Though it is quite odd that Peter and Mary Jane has no attaction to each other whatsover in that universe, I must say. Weird, but alas in the end we'd never know as that particular series will never be continued due to rights issues.
Other cartoon pairings I support include...
JacobXRenee (Jacob two two) - I usually don't toyship, but this was just too good to resist
AbeXJoan (clone high) - fuck Cleo, that self absorbed twat
TommyXKimi (Rugrats) - man, THAT episode just set it into stone my support for them
BenXGwen (Ben 10) - I personally have no qualms with cousincest