Stick with standardized codecs. In this case, Huffyuv
And not just Huffyuv
, but the normal one -- not 64-bit, multithreaded (MT), etc.
The only time I'd suggest Matrox codecs is for exporting from VirtualDub
as high bitrate MPEG-2 (10Mbps to 25Mbps). You're not really allowed to capture with the Matrox codecs. Nor would you really want to. Only capture with Matrox codecs if you're using Matrox hardware.
Some of this well be addressed in the capturing guides we're doing right now. In fact, there's several guides that covering intermediary codec use (aka "mezzanine formats"), including the benefits and downsides of various codecs in normal workflows. For example, you don't want to get stuck with a hard-to-use codec that's not future-proofed. Huffyuv is pretty well future-proof, and has wide acceptance all all modern platforms (including OS X and Linux).