If you find that your controller port has stopped working the culprit is most likely the fuse on the controller board. If it blows none of the controller ports will work.

Open the dreamcast case and remove the controller board. Be careful disconnecting the fan connector and the ribbon cable. on the top of the board you'll find what appears to be a resistor labeled F1 on the board. This is actually a .39A fuse Picofuses use the same color codes as resistors with an extra band at the end. This one is marked orange-white-silver-silver-green i.e. 0.39 and fast/slow blow spec. You can find a detailed guide with pictures here, however they incorrectly describe F1 as a resistor and tell you to replace it with a small resistor. This is a bad idea as the resistance across F1 should be zero and because replaceing it with a resistor removes F1's protective function.

I couldn't find any 390mA pico fuses but you could replace it with a 3/8 Amp or 1/2 Amp fuse from the Electronics Goldmine.