I have a couple CH Flightsticks (personal favorite) and a Flightstick Pro (haven't used much). Only 1 of those was mine since new, the others were found for $5 at thrift stores in better condition than my old one. They hold up great, even my old abused one is still very usable. I enjoyed it's accuracy in X-Wing and NASCAR, where lesser joysticks were just frustrating.
For other types of games, I like the old SNES style Gravis Gamepad.
There's adapters for using a 15pin joystick through USB. I got a cheap one from China a few years ago. It's been a long time since I used it, so I don't remember if it worked with all the buttons. I vaguely think it had some quirks with extra axes/buttons but I can't remember the details.
If you get a modern playstation style controller with the analog sticks, make sure the D-pad doesn't suck. Mine is so awful that I'm always better off using the analog thumbstick, even in games where I don't want to use it.
I think my ideal would actually be a USB conversion on a Genesis, NES, or SNES controller. I've never looked into it, but some box that converts from a Genesis input would be pretty versatile. There's lots of controllers that could hook up to that.