I've built quite a few custom ontrollers, and you really need a lot of depth to fit an actual arcade stick. My Amiga stick is built from a generic project box and 'american' style arcade parts that I salvaged from an old Street Fighter II cabinet.
The best thing about building my own stick is that I was able to add a few toggle switches for changing the function of the extra 2 buttons that I put in it. For games that only use one button, I switch them to 'up' and 'down' mode. It's especially helpful for platformers and racers.