MDK2 has a heavily annoying bug: the ADPCM decoder improperly handles clipping and produces click-like glitches, ruining the otherwise very good soundtrack. Additionally, the soundtrack is encoded in 22050Hz/stereo ADPCM which is not exactly top quality even without the decoder bugs destroying it further.
A friend of mine went through the trouble of acquiring a full ISO of the Dreamcast MDK2, ripping full CDDA audio tracks and patching them into the PC version, with downscaling applied to avoid the decoder bug. I have this customized version of MDK2; it's fully playable without any ill side effects that I am aware of; I can hand it over to GOG.com so you can apply these changes to the version you offer for download.
The same could be probably done with the first MDK game - the Playstation version includes high-quality CDDA music, but I'm not aware of anyone having patched the CDDA music tracks over to the PC version.

Sounds like a good idea. I think there are many games which would benefit from such things.
For a good example of how much an old game can be brought "up-to-date", check out The Ur-Quan Masters, which is an open source updated version of Star Control 2, based on the original source code. You can find it at http://sc2.sourceforge.net/

Hmm.. I get *no* clicks nor glitches in the sound whatsoever.
Probably due to my $5 onboard piece-of-shit Realtek audio chip, those have a tendency to work better than $300 Creative X-Fi-Whatever boards. Go figure.
Sounds like an interesting patch your friend did though, would be interesting to hear the difference. I doubt very much that GOG would bundle it up with the installer, that kind of stuff would be categorized as a "mod".

I agree, the music tracks could use a little cleaning up. I own the GOG and original PC CD version and its present on both. The PC version music tracks are encoded in interplay's acm format. To more easily hear the anomalies the poster is talking about here is an acm plugin for winamp.
A good example to hear this in is "Track01" or the main start screen track. Browse to folder "Program Files -> GOG.com -> MDK2 -> Music -> Track01" folder and open the file "track01a.acm"
At around 15 seconds you'll notice an example - plus there are "pops" throughout.
I have a copy of the dreamcast version also so I experimented with replacing PC version's music tracks with remastered ones from the dreamcast's CD-DA and all works well. You'll need a wav to acm converter to do so. If you use that utility make sure you rip the CD-DA in 22050Hz, 16bit, stereo wav (44100Hz produces timing errors). Plus the default parameter for compression on that utility is around 50 percent with the option to change it.
On a side note some of the tracks are slightly different on dreamcast version. For example, track01 is 3:33 long on dreamcast and 4:50 long on PC version.
To greatly increase the quality of the tracks it would only require 100MB extra or little less for space. I would be willing to do it for GOG also if they wanted. Although ideally it would be nice to have remasters from PC version's original raw assets considering the differences between the PC and dreamcast's versions. (whoever has those assets now)

I did some more comparison between dreamcast's and pc's versions of the soundtrack. The dreamcast's soundtrack compositions are heavily truncated by at least a minute per composition. This must have been necessary for space reasons.
For this reason it would be nice to have some form of the PC soundtrack to remaster from. Maybe GOG can get an mp3 version of the PC soundtrack from whoever has the rights now. Not only would it be nice to accompany the purchase here at GOG but would help those of us who would like to remaster the soundtrack properly for the game.

You have a bad pirate copy of the DC ISO, with truncated tracks cut down to fit on a plain CDR disc. My friend got one of those too before he managed to put his hands on the real thing. I also have untouched FLACs extracted from the proper DC ISO, with lengths matching what you get with the PC version.

What is the total play time for all 27 tracks on your dreamcast ripped FLACs? The PC version total run time for all 27 tracks is 82minutes 53 seconds. That dreamcast disc would need some serious capacity to fully support all that CDDA (already 11 minutes past the redbook clip of 72 min) and have enough room for all the game assets. It would seem that they would've needed to clip some of them at least for the dreamcast.
Edit:
The Dreamcast's GD-ROM format had the capacity of up to 1.2GB 112minutes so it could have had all 83 minutes. I'd love some lossless FLAC or Monkey's Audio from the Dreamcast version if it has all 83minutes of the CDDA.
I wish the composer Jesper Kyd would release the soundtrack for it. I'd gladly buy a CD version of it.

Total length of my MDK2 FLACs is 81:36.
I would preferably hand them over to GOG.com so they can be put in the bonus content section.
I could make them available in other ways (torrents etc) but I'm afraid that posting links to them here would be against GOG.com terms of service.

Thats close enough. I was thinking that even with 112min available on GD-ROM and the game assets taking up around 240MB that space would even be tight for 112min / 1.2GB with 83 min CDDA. I bet the minute and a half got shaved for space.
What sucks for me is I actually have an original GD-ROM of MDK2 for Dreamcast but can't find it. Most of the games I have for it I grabbed from used bargain bins, etc. after it's fall. I was working from that back-up because thats all I could find without purchasing another copy used online. Online used console disc sales is sketchy territory for me. I like to see the media if I buy it used.
Plus as a matter of practicality with the older hardware you almost have to move to emulation at some point. I always felt that if my door was ever kicked in over my atari 2600 roms - that the "My wife made me use emulation so as not to have every console known to
mankind tethered to the T.V." defense would work with any reasonable adult. :)
I was basically just thinking out loud when I said I would love a lossless format of the tracks. If they secured the rights to distribute the soundtrack with the purchase hopefully they would have access to the original PC assets or a proper encode of mp3 from them. If they secured the rights but needed the content you could still use a "public means of transport" (i.e. usenet or torrent) and still protect the copyrighted content by using a password protected archive. (i.e. password = gog.com). Since you can still be relatively anon on here I bet they would be hesitant over write access on a ftp of theirs. Plus most securiity conscience businesses' networks aren't friendly to P2P nowadays. Those FLACs are probably like around 400MB and if you didn't have your own private hosting you could still use "public transport" with password protection to securly deliver them to GOG.
I bet if Jesper Kyd knew how horribly encoded his beautiful soundtrack was in the shipping PC version he would glady "pony up" those WAVs for a re-encode by GOG. I still can't believe those encodes got past any kind of Q.A. Those encoding errors were avoidable even at the level of compression they used originally on the PC tracks. Considering they (Bioware) had access the official dev kit tools for interplay's formats and it only takes 82minutes of man-power time to properly Q.A. the encodes for those tracks, there's no real excuse as to why they turned out as horribly as they did.

I have a simple archive that contains only the updated ACM files (ripped from the Dreamcast version at 44.1KHz and several modified for pops or other errors at the start of the tracks, and all files are peak scaled so they don't trigger the decoder clipping bug) and the v4000.3 mdk2Main.exe modified to play the files at the correct sample rate, as well as forcing 24-bit Z buffer to fix some graphical glitches. It comes to about 400MB, and I don't really have anywhere to host the content for mass downloading, nor do I have permission to redistribute the files. Now if only we could get some support from GOG staff to distribute this as bonus content. Hmm...

Any news on this? Have the files been updated yet?

kode54, can you detail how you modded the game with higher quality audio so we can try to replicate it?