I found a lot of things I hadn't thought of before in the PxTone manual. Half the manual explains how to use the program (a free sequencer program made by the developer of Cave Story) and the other half goes into how to think about video game music, as well as specific examples from songs that come with the program/manual. It also shows how to work with chiptune arpeggios like it was done in the 4-bit and 8-bit eras.
Other than that, from my own experience I like to look for an existing track that has the right mood for what I'm working on. And then try to do something original using a similar tempo and a similar speed of melody, often listening to only the first couple of chord changes to get a feel for the dynamics of the track.
PxTone manual (including the software) can be found at: http://www.gr87.com/?page_id=64