Sometimes other tools come handy, too; the mcu is almost never an isolated chip - it has some peripherals connected. An oscilloscope and/or logic analyser laying around is invaluable. Sometimes it is good to have task-specific tools, various protocol analysers have been mentioned here (e.g. for USB). A set of cables with the wildest combination of male/female/straight/mirrored/cross/loopback is always good to have when working on serial communication devices.
At the moment I am working on a protocol conversion gadget; having a tool capable of capturing and displaying fullduplex serial communication in a smart way would save me a lot of time (I consider building one).Also, as already two UARTs are occupied, I am spitting out the "debug printouts" in a soft-UART manner, but at a fast rate (4 cycles per bit, it's a 12-clocker at 22MHz - this does not significantly ), with an extra "1" startbit (enabling to autobaud on any single byte); capturing it by an another board (being this my custom tool :-) which then retransmits it via normal UART to PC.

Jan Waclawek