I know I still need to write about when and how, but here are some of the smaller thoughts that didn't seem to each need their own full post.
What are you bringing? Think about what you might offer in addition to what you want. You may have a mailing list, or a connection to a caterer, or a car that is appropriate for the 1970's time period of the indie film. Something that you have that they need might help you get what you want.
Unions - if you're in one, they've already done a significant portion of the negotiating for you - minimum salaries, size of dressing room, you name it. If you're not in one, you should still go to the union websites and find the info about pay rates and contracts. Start here for Actor's Equity. Then look at the 'codes' and 'agreements' Screen Actor's Guild (SAG) won't let you look at the full contracts, but you can see summaries and rate sheets here. AFTRA rates are here.
With non-union on-camera projects and industrials, knowing union rates can help a lot with your negotiation. The person making the industrial may not know a lot about what the rates are - starting from 50% of union rate as an offer on your end is often a good way to go.
Usage - with camera, voiceover and print, the question to ask is what are they using this for - where will it be shown and for how long. Are they asking you to give them usage rights for a limited or an unlimited time? For a limited or an unlimited geographic region? web only? cable only? The fewer limits to usage, the more careful you need to be about taking on the project.