Wow! Just about everything you've posted matches my own situation. Even the desktop speakers. Apart from the MB outs, though.
If a good, (read really good) USB or 1394 DAC is purchased, ala Wavelength; Weiss, etc, that route is definitely a solution whorthwhile.
I use a Bel Canto DAC 3.0.
I've tried each and every route to feed it likewise files as you described. Ultimately using the Lynx AES16 PCI eXPRESS CARD and AES connection in conjunction with Lynx own ASIO out & either Fubar or JR MC (current versions), to achieve my best sound thru a MAIN audio or HT system.
Many of my posts on PC audio point to my above comments if you care to peruse them, or if you can presently. I'm having issues with this new site upgrade personally.
Each link in that signal path from the cable, interface, and output device & DAC will help or hinder your ability to achieve a great solution.
For ex. I could upgrade my cable from the Lynx to the BC DAC3, as I feel it is my weakest link. Naturally upgrading the BC DAC3 to 3.5 status would likely be as well a fine move. Thereafter, all of the downstream components fall into line for consideration to replace or update.
The DAC IMHO is the true key.
That said, each segment thereafter really does matter.
Final note.... Multi interface DACs are in general better sounding using one of it's interfaces over another. Mine is limited to 16/44 on USB I think, so for me, USB out is not a solution. Coax sounded better than TOS, and AES better still than any others. So it behoves you to experiement for yourself.... unless of course you select a dedicated interfaced DAC. Then only the cable itself requires messin' around with.
Good luck.