I figured out the cause of the bug I was talking about before which causes Camstudio and MLC to lose their settings in some cases. Both codecs use an antiquated API which writes ini files to the windows directory. In Vista\7, this is emulated by the "VirtualStore" feature. For some reason it doesn't work right in this case, but considering the API in use was obsoleted in 1995, I can hardly blame Microsoft for that one.
If you're technically inclined, the issue can be worked around by setting up a registry ini redirection as outlined here:
http://msdn.microsoft.com/en-us/library/windows/desktop/ms725501.aspx
Of course, it doesn't change the fact that MLC is as slow as balls; but it's the best solution for emulators that have buggy 2GB split code.
I've created a VFW "codec" that pipes the uncompressed data to the process of your choice, which can then compress it externally. Unlike most things I do, this actually seems to work rather well.
Unfortunately, I have nothing to use with it yet: it's apparently quite difficult to properly import lossless RGB x264 into avisynth. FFMS2 gets the colors wrong, and DirectShowSource + LAV filters has seeking problems.