The only downside to VLC is that it is _not_ the default media player for Windows, which means it is not the program that the PS3 talks to when looking for media servers.
I just spent a little over two hours...
1: Installing the Divx codecs so Windows Media Player could read mkv files
2: Getting WMP to actually realize it could now read mkv files
3: Installing the AC3 filter like Divx said i ought to when some of my mkv videos didn't have any audio, which didn't work.
4: Using VLC to discover the files in question were using FLAC for their audio component.
5: Installing the Xiph codec to handle the flac part, which didn't work
6: Installing the K-Lite Mega pack to handle the flac part, which didn't work
7: Installing the x64 version of K-Lite to handle the flac part, which worked!!!
8: Realizing that it only worked if i right-clicked the file and ran "open with" and selected the _second_ WMP listing, not the first, and _not_ if i ran WMP from the Start menu
9: Figuring out that the second WMP in the "open as" list was the x64 version, while the Start menu version was x86
10: Running several registry hacks to change the Start menu WMP link to the x64 version
After all that, mkv files show up in Windows Media Player, and all the ones i've tested so far have both video and sound.
...and still doesn't have any sound when i play it on the PS3!!!!!!!!!!!!!!!
I guess the PS3 uses the x86 version regardless of what i have the default set to on my machine? Or there's something else screwy? I don't know, but i think i'm giving up on it for tonight, perhaps i'll work on it some more tomorrow =P