If you're running a home studio, essentially its your time and your gear, so you can pretty much charge by the hour, or by the song, or by the album, or by the day/week or whatever. No harm in this whatsoever.
If you're running a pro-studio, there are a lot of factors.
Are you the engineer? Are the artists/record company providing the engineer? Are the union?
What are your per-hour costs to keep the doors open and the lights on? Are you booked 2-3 weeks in advance? Or are you begging people to come in?
what are your competitors charging? (very important).
I've never professed I'd be the least costly studio around (when I finally get to building it - have the building and most of the gear), but charging double what your three neighborhood competitors charge is not necessarily a good thing.
Case in point... where I'm eventually housing my pro studio, I've found four competitors within a 15 minute radius, three semi-pro and one is a home studio.
The home studio guy is all analog, and a lot of really nice, older gear that produces real nice sound. he charges $60 an hour with him as the engineer.
Two of the other three are hybrids... digital recorders (adat or hard disk) with mackie analog boards and no mastering ability that I could hear. (I saw gear, just not the expertise).
The fourth is going to be a thorn in my side. Protools all around, digital everything, the guy is older, experienced, and probably knows every trick in the book. Being retired, he charges $45 an hour with him as the engineer.
Since I own the building my studio will eventually be in, and 1/2 of the space is currently rented out for a bag of pretty penny's, I can afford to keep the doors open indefinately whether I have clients or not. This is why semi-pro home studios are often successful - less overhead.
The bigger the studio, the more people you need to run it, the more lights, larger electric bill, etc, you need to put all that fixed costs together to determine what you really need to charge, assuming you're running a pro studio.
Hope that helps!
Frederic