For indie films, usually we agree on 5-10% of the film budget depending on the initial spot and how much music we feel the piece is going to require. Mainstream films of course are a smaller percentage since their budgets are usually gigantic. Though I’ve yet to have the pleasure of scoring such a film 
For sound design, more complicated projects are usually hourly based (maybe Im the only musician left on earth that has an option to be paid hourly)
Single songs are a mixture of a licensing and work fee, the license is a flat rate and the work fee can be hourly or decided before starting the project.
I haven’t had any experience with television yet but I believe most people charge per minute of music. + Royalties
I agree with Thomas, negotiating with the client is the most important thing especially when you’re starting out. People have a wide opinion of what music is worth to them. One client might be shocked and run and hide under their bed if you quote them $5,000 to score a short film. Another client might have been planning on paying $5,000 and be shocked when you quote him $400.