This is an excellent GUI for free video encoding/muxing components and it has both 32 and 64 bit versions: FAVC
I use it on Vista64 with Shark's Vista Codec Pack and in Windows 7 7077 (the 32 bit version of FAVC) with Shark's Windows 7 codecs. What's really cool is you can set it to launch an encoder for each CPU core. When I convert a video file on my quad core it analyzes the file, breaks it up into 4 pieces and launches HC(you can use QuEnc if you prefer but HC "predictive quantizer" mode gets almost as good a result as 2 pass HC at almost as fast a speed as QuEnc single pass.. I've been using it exclusively lately) encoder for each piece, for each file in the list. Very good quality results.
edit: to see the difference run Core Temp or another performance tool that shows your core usage stats, then run a multi-threaded converter. Then run FAVC. You'll see that with FAVC all your cores are maxed out instead of getting maybe 68% average across the cores with multi-threaded apps.