Not really ultimate set ups but my preferred setups at least. I use the best cable types I can for each system natively, no video mods so far. Off the top of my head these are the consoles ready to go.
AV Famicom with cart converter
Regular Famicom
NA Master System model 1
JP Master System model 1
PC Engine briefcase unit with white CDrom2 and CG1
DUO/DUO-R
Supergrafx/SuperCD vacuum cleaner
SEGA/JVC Wondermega model 1
NA Model 1 Genesis/Model 1 Sega CD combo
SNES
Super Famicom
Skeleton Saturn
White Saturn (to play the ones the skeleton can't)
JP Dreamcast
NA Dreamcast
Modded PS2 (to play DVDRs)
PS3