I've had luck with the Microsoft Sidewinder (USB Version)...
It's kinda neutral & has 4 buttons on top & 2 shoulder buttons.
I'd probably go with
this one though...
It's got more buttons... (Start, Select, 4 shoulder buttons & 4 main buttons)...
I know it's more like the PS controller, but it's the only way to play PS games (that require the shoulder buttons)...
Or you could just hack the original controllers to a USB controller & then you could use the original controllers for all those games. Just hack a coupl of USB controllers into a project box with a couple of DB15 ports on the fron to connect your hacked console controllers... It wouldn't be too hard & you could pick & chose which controller to use! (you could even build a small arcade controller box for it!)
ok... ok... I know... I'm getting carried away...
OT...
Are you going to build a little Shuttle PC? I love those little cases with the handle on top. That would be ideal for what you're doing. It's even got TV-out built right in. You'd just have to set up your front end to start up right away & it would be a sweet little console...
Hm... Oh Great! Now I've got another project on my never ending list!!!