A true 5.1 system with excellent speakers and sub will reproduce exactly what the audio director intended for the Dolby DVD edition of the movie. Although you can't expect "excellent" performance in 5.1 for less than at least $1000 for the speakers alone, the available computer systems like Klipsch and Videologic do very well in DVD performance *for the price*, as long as you sit within a few feet of the drivers. But I think only Klipsch offers a good 5.1 computer system. Forget Cambridge Soundworks, I've listened to their systems and I've never been impressed.
The quality of 4.1 sound in DVDs will depend on the quality of the downmixing algorithms used. I've heard that the latest software decoders like PowerDVD XP 4.0 do a pretty good job at downmixing. However, it can't sound as good as keeping the channels separate because this mixing has to be done "on the fly" as the DVD is playing, which means there will be compromises in the final downmixed quality.
A 4.1 system will, to some degree, compromise the quality of the front channels because the software is attempting to smear the center channel into the two fronts *while simultaneously decoding the audio and video in real time*. My guess is that, especially during heavy action scenes where all channels are playing, in the fronts you will lose some dynamic range of the signal and possibly some audio clarity as well. The degradation will probably be noticeable to an audiophile or serious audio enthusiast, but to most people it won't matter. Perhaps when 5 GHz CPUs come around and the downmixing algorithms are refined further, the software will be able to do it without any noticeable loss in quality.
Of course there's also the matter of losing the anchoring of voices and other sounds directly in front of you. But this is relatively minor on computer speakers because the separation between the front channels is small enough that a phantom center works pretty damn well! The main issue here is the final downmixed quality being inferior to the true 5.1 experience. But again, if you're not serious about watching DVDs on your computer, all of the above is just not a big deal.
Ritesh