Agree to a point there. It all depends on the quality of the DAC/system setup. It's the same as the difference between a crap CD player and a good one. I'd quite happily put my Mac/DAC up against any CD player on the market.
Moving on, some constructive help. To get the best out of your Mac which might eliminate the Mac being the culprit as opposed to the rDAC not being up to scratch.
Download a free trial of PureMusic or/and Amarra. Itunes SQ is crap and can easily be improved upon. Both are pretty decent bits of software and everyone's got a preference as to which one they like better so please no 'PM is better than Amarra' or vice versa as it's all down to personal preference. For me i like PM. Use memory play so the tracks are loaded into the RAM for playback and enable hog mode for usb playback.
http://www.channld.com/download.html
http://www.sonicstudio.com/amarra/amarrasupport.html
Disable Spotlight on the drive with your music. (Your internal from the sound of it?). Takes about a minute to do and stops it indexing in the background.
http://osxdaily.com/2009/09/20/disable-spotlight-in-mac-os-x-10-6-snow-leopard/
(the terminal is in applications-utilities-terminal)
Disable the Dashboard. Again easy to do. Another background task that you don't want running and can hog memory.
http://osxdaily.com/2007/03/14/how-to-completely-disable-dashboard/
(again through Terminal)
Go into energy saving preferences and put computer and display sleep to never. Also disable put hard disk(s) to sleep.
Turn screen saver off.
Turn off automatic software update.
Get iTunes set correctly as previously mentioned. Disable sound enhancer/soundcheck and stick the volume to 100%. Make sure the EQ is off as well.
Again as previously mentioned go into applications-utilities-audio MIDI setup and make sure your output is set correctly. If you use a mini-toslink - toslink cable download soundflower and use that to run your output.
Rip a cd in AIFF/FLAC. If you can and have access to a PC use dbPoweramp/EAC to rip the CD so you know its an accurate rip. PureMusic will play FLAC through itunes if required. Good guide for dbP can be found here:
http://www.computeraudiophile.com/content/Computer-Audiophile-CD-Ripping-Strategy-and-Methodology
Lastly try and not have any external storage devices connected through usb when your using usb to rDAC.. If you need to try and connect them with Firewire if possible.
Don't think there's much more to it on the computer side. If anyones got anything else to add feel free as i'm all ears.