First step, I listen to the tune for half an hour to an hour away from my bass through ipod
I run everything through my computer, I have a USB interface or sometimes I use my Pod footboard into the computer for my bass. I have 2 nice sets of headphones, a sweet set of studio closed ear style 'phones and an old Sennheiser open air set, both work great. Then I load the song in Transcribe software (about $50 I think). Very nice, you can mark sections/measures, loop stuff, slow down without changing pitch if necessary, and full equalizer to isolate certain parts you want to hear better. Then I use Sibelius G7 software to write out the part once I've figured it out. It has a playback mode so you can listen to what you have to see if it sounds right.
Sure beats the old days with a cassette and pen and paper.