I'd say that the best controller would be to use a real N64 controller, and while the adaptoid is rather expensive, you should (with creative Google searching) find a N64 to USB adapter for a LOT less than you're finding that will interface well with default joypad plugins for PJ64. You might have to do some calibration to get it "perfect", but that'd be the best controller.
As far as my opinion, I purchased a Radio Shac brand PS2 to USB converter ($12) and am using PS2 controllers with almost perfect results (the rumble is ~slightly~ off).
If you want cheap, you might suffer quality loss, as well as the "break down from wear and tear" problem with the cheap-o controllers out there.
Bottom line though, get something comfortable for YOU, and work from there.
As for Random_Guy's question, go to your Controller configuration (Options>Configure Controller Plugin) and then set the controls to your liking.
I recommend that you set the Arrow keys as your analog, Num0 as B and NumDel as B and the Home/Delete/End/Page Down as your C buttons. You can ~also~ set up the Analog's "Second configuration" to use alternate buttons (Config 1/2) so that you can keep the Digital Pad's configuration ~also~ as arrow keys in ~some~ games (Tetrisphere, ect).