Well this is quite disconcerting to hear. I really wish apple would get their heads together and make a native desktop audio capturing API so users wouldn't have to go through this.
Okay, did you guys double-check the settings? In the vast majority of these cases, the problem is simply that you lost your configuration somehow, especially when reinstalling them.
Try this:
1.) Go to system preferences, then go to Sound
2.) Click the "Output" section
3.) Select your speakers or headset or whatever device would normally be your output
4.) Now, make sure that it is unmuted at the bottom. This is important. It must not be muted, and the volume must be up on your actual device, otherwise it will not capture.
5.) Now select Wavtap or Soundflower (2ch) (note: do not use 64ch! It will not work.). Make sure this is unmuted as well.
6.) Exit system preferences.
7.) If using soundflower, open soundflowerbed, and configure the 2ch section to use your speakers as an output. I don't know if wavtap has something similar, but if it does, do the same there.
You should then be set up to capture again if you follow these steps.