I use percentage most of the time, but have a couple of programs where I take a mix of both.
The CPA programs seem to have come a long ways since when I started and I think they are a lot more fair now.
If you are just getting started CPA can give you capital to work with. If you are in it for the long haul, percentages are better.
If you are dealing with bonus hunting – that really isn’t profitable for affiliates over all, and you are likely better off with CPA then.