I've got three:
Proline SI Edition (Atari7800): One of the running projects that everyone's heard about. I finally took the plunge late last year, and it's rapidly become my favorite stick. I've thought about picking up more of these for future projects.
Sega 7800 Joypad (Atari 7800): One of my 'extra' Genesis 3-button pads, reworked to two-button compatibility on the 7800. The key bitch was having to cut off part of the ground so that I could properly rewire it. I also found out that there are two variants on the circuit board, and only one of them wasn't surface mount.
Fighter's Choice Stick Rebuild (PS1): I didn't want to throw this one out when it died (I didn't have the Radica Gamester at the time), and I had a spare Sony digital controller floating around that I wasn't going to use. In short, a new brain for the stick, and it works like the day I got it, except for the (useless) autofire option.
Anyone else have any custom controller projects that they've undertaken?