Sand it down and glue on a PlayStation-style nub. (You have dead controllers to salvage, I know it.) I've seen it done before, and it looks comfortable. I actually LIKE the default controller, though, save for the fact that one of mines doesn't have a fully-functional expansion slot. (It likes to erase rampaks.)
... While we're on the subject of N64, would there happen to be a way to create a rompack? It would save me so much trouble. At the moment, I'd have to play through Lego Racers or Doom64 in one go with limited breaks to ensure that I don't even need to worry about losing a save file to begin with. I've lost saves while the console was still freaking turned on.
Personally, I use a nothing-special-in-particular gamepad with six face buttons; THAT'S what one should use when playing an emulator, particularly one for older consoles. The only thing wrong with it is not having an equivalent of the Z-button, but I've heard (From Benjamin Heckendorn nonetheless!) that so few games use the L button that one can safely map it there.
For everything else, there's the 360 wired gamepad. (I kinda wish I had the official one, but I can say from experience that the MadCatz version is actually quite better excepting a lack of sensitivity in the triggers.)
Grim: You want a Gamebit. Alternatively, you want a whole new power supply. IIRC you're decent with a soldering iron, so you ought to go for the bit. Chances are you only blew a capacitor anyhow, and the same bit opens lots of console things. (Links go to eBay, by the way.)