Just FYI, a new version of PerfectNotes has been released.
PerfectNotes lets you bookmark your audio file just like the post by markfoley mentioned. You make bookmarks as you go, whenever you hear something you want to come back to. Then whenever you have time, just click your bookmark and hear it again. It makes it so much easier to jump around the audio file. Plus, you have an instant visualization of not only what you wanted to hear again (your bookmarks), but a visualization of when people were talking along with markers showing what you typed. It's all put together on one timeline.
You can also be anywhere in your notes, click a button, and it will instantly load the audio file to the general time when you made those notes. So you can look at your bookmarks to see what you wanted to come back to, or at any time you are confused on your notes, you can click a button and hear what was said.
You don't have to take notes in PerfectNotes either. You can set it to record and then minimize it. You can be using any other application, and when you hear something you want to bookmark, you can then click on PerfectNotes, make a bookmark, and minimize again.
A lot of people have found it to be a great note taking tool. It's pretty amazing being able to just click and hear what was said. Feel free to try the demo, available from www.PerfectNotes.com