Okey, so what I've gotten out of this thread so far is that most of you guys don't dig deep enough. File associations in itself can't contribute to changing a DirectShow filter merit. However, if you set the file association within the application (e.g. WinAmp or Windows Media Player), it might also change the filter merit. Thus, the problems lie with the game using the DirectShow filter with the highest merit, and not with file associations nor the merits themselves.
Problems with DirectShow merits is nothing new, it's been haunting us for a long time with many developers doing the same mistake in the past. So this whole situation is disturbing to say the least. Why oh why did Bethesda not think of this? Why does the game use DirectShow filters based on the highest merit? It's just plain stupid, and considering that there are hundreds of different filters and codecs out there it should be something the QA-team would have tested, right?
Anyway, you don't have to uninstall or disable any of the codecs. The best way is to use an application like DirectShow Filter Manager (http://www.free-codecs.com/DirectShow_Filter_Manager_download.htm) and change filter merits and debug which codec works and which do not, because Fallout 3 will use the filter that has the highest merit. Most likely it should work best with the "default" filter merits, but other filters might work better, or as in many cases just break the game by introducing stuttering, missing audio/video or even BSODs.
For more in-depth info on DirectShow merits: http://msmvps.com/blogs/chrisl/articles/40395.aspx
I hope this helps shed some light on the true reasons behind this problematic but yet simple situation.
I've been poking around in K-Lite, and have found you can change the merits in the 'Gspot Codec Info tool'. System>List Codecs and other filters>Rightclick>Set filter merit. (For those comfy enough to do so. [P.S.] It's just a slider bar.)
0x00200000 = Merit_Do_Not_Use
0x00400000 = Merit_Unlikely
0x00600000 = Merit_Normal
0x00800000 = Merit_Preferred
You can also 'batch disable' in the Codecs Tweak Utility. Just scroll down and select what you want to disable.