I'm trying to figure out how much improvement I can get by upgrading from an Onkyo 2 channel 50w/per channel .08 THD to a more expensive (quality) integrated amp from NAD or Rotel (these would be somewhere between 60w/channel and 120w/channel).  They are selling used for $250 - $400.  I'm running Energy C-3 bookshelf speakers with an 8" Energy 100w powered sub.  Thanks for any advice.

I think you will be surprised that the difference is not that great.  I previously owned the Onkyo 100 watts/channel stereo receiver and replaced it with a Cambridge Audio stereo integrated amp, thinking it will improved the sound quality.  However, I found the difference to be minimal....certainly not worth the difference in price between then receiver and the amp.  On top of that, I lose the convenience of having a tuner and a phono section.

If there's any difference in sound whatsoever, then one of the units is defective.  All an amp does is take a signal and amplify it to a speaker-level current.  It's not rocket science and if it's doing anything to the quality of the sound, then it broken (or you've adjusted bass/treble which is pretty easy to remove the influence of).  Every scientific study ever done shows clearly that a cheap amp cannot be ABX'd from the $30,000 crowd.  The only reason to spend bigger money is for an amp capable of driving low-impedance speakers (which you don't have).

Start reading here (there are a ton more tests on the foreign-language part of the site):

http://www.matrixhifi.com/ENG_marco.htm