I have recorded at 44.1, 48, 88 and 96. I can't tell any difference between 88 and 96 (so usually use 96kHz between the two, personal choice). Between 44.1 and 96, as much as I kept telling myself that theory says I shouldn't be able to tell them apart, I actually can on the drums, namely the cymbals. At 96kHz the cymbals seem to sparkle more.
On the gearslutz forum do a search for sample rate. There were many tests and some top engineering and gear designers have left comments. Basically with today's algorithms it seems that you shouldn't worry about 96kHz to 44.1 or 48 to 44.1, the conversion will be fine (i.e. no need to use 88.2 so that it's nicely divided etc). As far as using 96kHz, the aliasing curve is smoother than at 44.1 and this would be why 96 sounds better than 44.1.
I left a lot of details out so if you want more do the search as I mentioned above.
Cheers,