I know my tests aren't scientific but I remember listening to some home
audio receivers awhile back.

I was looking at one that was 100W X 2 . It was on sale for $300 down
from $400. I listened to it to it and I was gonna get it, then, my
friend with me said "try that one over there". A $250 50W x 2 amp.
After listening to the same song on the same speakers with the 2 amps I
am absolutly certain that the small one sounded better (in the higher
freq's anyway) so that's the one I bought ...at full price.

You guys that argue there is no difference, power is power...How do you
explain that there was an obvious difference?

There are a number of reasons, and they've all been outlined in this thread
so I won't rehash them. But in your case, don't be fooled by power RATINGS.
It's one of the tricks (in car audio at least) that more expensive amplifier
marketing departments use to give the impression that their amp is better.
That's why some companies underrate their amplifiers.

Can't one amp have a more
linear frequency responce than another?

They can, but if you test them, you'll find that they don't.