ajdolby, don't give up on Perian.. it's not spyware, it is a System Prefences control panel and will end up there, in the bottom row (the 'Other' category)and loads into your Home/Library/PreferencePanes folder. It's a Godsend, though it does NOT work with QuickTimeX - that's as Apple has completely rewritten the 'Core A/V' and it's all 64 bit now, whereas Perian is 32. Don't be run off by that, though. With the correct setup and the right programs, you can have almost any video format running.
If you're still having issues, and need QuickTime (I use it almost exclusively since it can step frame-by-frame and I make screen grabs for my graphics projects) your best bet is to install QuickTime 7 and add all the codec packs.. Here's my cut-and-paste tutorial with all the links to get the files you need so every thing works.
You need to install some other stuff to get the full file functionality back.
Here's the list.
Start with QT 7.6.6. - http://support.apple.com/kb/DL923 (This will install into the Applications/Utilities folder)
Get Perian, and install it. - http://perian.org
then VLC, - http://videolan.org
and the Flip4Mac package from Telestream - http://www.telestream.net/flip4mac/
A52/AC3 downloader: https://www.macupdate.com/app/mac/21875/a52codec - In this installer package there is an audio A52Codec.component. DO NOT USE IT! Throw it out and use the one that is linked below.
This is what I've put into my system and so far I've gotten every file to run fine, even my oldest videos.
These are codecs you should see.
In System/Library/QuickTime
AppleIntermediateCodec.component
AppleMPEG2Codec.component* (*optional if you've bought it)
Flip4Mac WMV Advanced.component
Flip4Mac WMV Export.component
Flip4Mac WMV Import.component
In your Home/Library/QuickTime/
AC3MovieImport.component (you may or may not want this component, in some instances it causes conflicts. In my system, it doesn't. Who knows why? I don't.)
Perian.component
For AC3 sound that is in most .mkv files, you need the A52Codec.component, this is the one you want, here: https://code.google.com/p/subler/downloads/detail?name=A52Codec.component.zip - unzip the file and put the component into the System/Library/Audio/Plug-ins/Components
Go back to your Perian settings (It should be in the System Preferences, at the bottom) and in the Audio Output button, set it to 'Multi Channel Sound' - Ignore the message Perian puts up and select it.
By doing a 'Get Info' on your files and where it says 'Open With' - default them to the QuickTime 7 program. Perian no longer will work with QuickTime Player so you must have QT 7.6.6 and set it so it is the default for all the filetypes you use.
If you DO decide to do this, just do NOT delete the QuickTimeX. For some reason, the OS get's a bit peevish that it is not there anymore and it's a real pain to have to re-install. Just leave it.
Everything works perfectly with QT7 - and you CAN buy a Pro Key from Apple if you want to unlock it and access it's full editing/transcoding capabilities.
So far I've gotten ALL my old videos to play.
.avi, .mov (with the AC3 sound), .wmv, .flv, .mp4 and .m4v. all run fine as do all the older formats.
Good luck!
Deb.