Whooohh...
If you haven't noticed, windows make hickups when you insert a CD in the tray.
This would mean that even though you had a program that could mix two CD's, then you wouldn't be able to change CD's while the other was playing.
What you could do was getting a program that mixes MP3's.
Then simply make your own "virtual CD's" on the harddisc and you are ready. It is also easier when it is all in the same place.
I've tried it once at a place with virtually no room for any gear = (computer and a tiny mixer).
Beat-matching isn't very easy and you have to have two soundcards or have a hardcore program. Other than that, the sound is just as good as direct play from the CD's.