I've been trying to figure out how to connect my BBB to my RPi but it seems Raspbian lacks the RNDIS drivers, or something like that. Has anyone done this? (And has anyone found a real reason to other than to say they did?) It does seem capable of powering the BBB, but having to connect through Ethernet seems like doing it the hard way.
It depends what you want to do with them, both should be capable of using GPIO to talk using I2C, SPI or UART (serial).
If you are intending to transfer large volumes of data then Ethernet may be the best option, if you really care about latency then maybe just raw GPIO bit-bashing (manual software control) would be best, for most things either I2C or SPI would seem most appropriate (SPI is faster but uses more GPIO pins).
If you provide an idea of what you would like to actually have them do then we can probably give you a more specific answer.