I use my DVD player for CD's via fibre out, meaning if I had a CD player with fibre out as well, there *shouldn't* be much difference since the AV Amp is doing the decoding and treating the DVD/CD player as a transport anyway.
Comparing a Pioneer/Panasonic DVD etc with a NAD or higher CD player with fibre or internal decoder out I can't comment. The difference might be huge.
It also has alot to do with your reciever.
If you had a higher end Marantz or Denon reciever, and hooked up your middleroad Panasonic or Pioneer CD player to it, the digital out will sound better than the left/right channel out of the CD player since the decoder in the reciever is being used which is likely better quality than the one inside the player itself.
But if you're using an audiophile cd player, I'd bet my money on the player, instead of the reciever's decoder.
Something to keep in mind if you use the DAC in the CD player.
The majority of receivers convert the analog signal back to digital to perform bass management and other DSP functions. Then converts it back to analog. And some receivers even do the coversion in direct mode or they loose all bass management fucntions. It seems to me that there is too much going on in the signal path when you use the CD's DAC.
Also be aware that a lot of DVD players can't play CD-Rs and/or CD-RWs; almost any CD player will play CD-Rs. If burning your own CDs is important to you, make sure you're looking for a DVD player with CD-R/RW playback capability; if you've already got a DVD player, and it doesn't have this capability, then it might make sense to buy a separate CD player -- especially if you step up to a 5-disc changer or 300-disc jukebox, which would have the additional convenience factor going for them.
And to reiterate the advice above: if your receiver doesn't have an analog direct mode to send the player's analog signal directly to the volume control (i.e. bypassing all analog-to-digital and digital-to-analog processing steps), then you'll want to send the digital signal out from your player and let your receiver do the digital decoding. In this case, it really just won't matter much what type of player (DVD or CD) is "spitting out" the PCM bitstream. Hope this helps!