48K gets used for several reasons...
Audio for DVD video should be 48k.
Some soundcards (Creative for example), only actually run at 48k. It is better to record and mix with this rate and use the DAW or editor program to do a final conversion to 44.1k for CD.
The projects audio may have arrived on 48k media (DAT, Minidisk etc).
If the card also supports 96K (higher Audigys do 48 and 96), a rate conversion to 44.1 will be more accurate from 96k.
Clues for Audio interfaces that only do 48 and 96, is that these will be the only rates provided by the ASIO driver and s/pdif output.
DirectSound and Wave(MME) are not always trustworthy, because Windows provides an SRC (sample rate convertor) for these. Creative cards also use their built in FX DSP to carry out the SRC. Neither of these will be as good as dedicated audio software at doing SRC.
As for working at 96k (or 88.2), the best reason I've heard is that it sidesteps issues with the soundcards converters. Most converters have a "brick wall" low-pass filter to stop them handling frequencies close to the sample rate (anti-alias). The filters work at half the sample rate. Unless very well made, these filters cause audible artifacts due to phase shifts. This is not obvious with standard equipment tests like frequency response or THD - you have to hear it.
The Anti-alias filter side-effects occur around the cut off frequency. With 48k this would be at 22k and so artifacts extend into the audible range below 20k. With 96K, the filter's at 48K and far fewer, if any, artifacts extend down below 20k.
If we go even higher and use 192K, the converters filter doesn't need to be a "brick wall". A gentler roll-off shelving type can be used which should be far more benign.
If you'd like to read a book on the more esoteric aspects of all this, have a look at "Mastering Audio" by Bob Katz. I'd warn you that although it's not a technical engineering book full of formulas, it's still not an easy read!