I have several core clients for whom I do ongoing work. They tend to feed me stuff on a very regular basis, and I just bill them at the end of each month for hours worked, regardless of whether or not I'm half way through a particular project. It keeps their payments regular and manageable and suits them and me.
I use freshbooks.com for the time tracking and billing, and my clients all have a login that allows them to monitor how the hours are stacking up. They really like it and being able to see the hours as they update each day really seems to reassure them that they're getting a fair deal.
Clients I don't have an existing relationship with, I tend to steer towards a one-off fee based on the brief. Firstly it gives them a concrete figure that they can budget for - there are no unexpected overruns. Or, if I get the job done more quickly than I expected it's a little more profitable for me. The figure is usually based on my expectation of how many hours it's going to take, rounded up to the nearest full day (unless it's a tiny job, but I tend not to take those from new clients unless I'm convinced it'll lead to something bigger).
My standard fee is 6,000 yen p.h. for programming (about $60) and 5,000 for design (about $50). But occasionally I'll vary it depending on the client. That's not a great indicator though. The cost of living, salaries etc. are different in Japan and don't really compare, especially given the fluctuating exchange rate at the moment.
It looks like things are about to change though. My biggest client has been asking me to work for them for several months now, and they've just increased their offer to the point where the money is just too good to say no.