Bela uses all the pins highlighted here for the 16 digital I/O and then pin 24 on header P8 and pins 10-15-17-18-19-20-21-22-23-24-25-26-27-28-29-30-31 on header P9 for communication with the board.
The multiplexer capelet additionally uses pins 40 to 46 on P8
Check out the pin diagrams here to see what is left available, note that some of them are in use by the system.
Also note that some of the available pins may require you to change the pinmuxer in order to use them as GPIOs or analogs. The website with the pin diagrams is the most exhaustive guide on the BBB I could find and has all the resources you'll need.
Also note that the BBB's own analog inputs, besides being slow, low-resolution and noisy, also have a maximum voltage of 1.8V. If you exceed that, you can trash your BBB.