Lately I've been trying out a software that's been around a couple of years.
Quick AVI Creator. It's a freeware:
http://www.videohelp.com/tools/Quick_AVI_Creator
It has both encode with xvid 2 pass and encode with x264 3 modes to choose from.
Also it's simple enough to edit the xvid.presets to add an xvid "One Pass Mode"
I've done a few conversions using xvid both downsized to standard DVD and with HD output.
The results look good even with my "one pass mode."
The last couple of runs I've been trying out compressing .mkv.
I've only done a couple of runs. One is going on right now. But
I'm optimistic it will turn out to be a viable alternative to Handbrake.
It uses AvsP so you can tweak your filters.. and it does the basic stuff for you like
setting the correct color space etc..
edit: I did successfully compress a 90 minute film using this app.. took 10 hours on my dual core for
x264 one pass. I noticed the audio just slightly out of sync but that may be due to telling it to
use the audio track as is... could be fixed easily enough by adjusting audio delay I'm sure.
From my trials so far, the most bang per buck with this app seems to be converting to
.avi HD using xvid encoder with one pass mode. The runs I've done using 3200 kbit
for bit rate have come out quite good. A full length film ends up being a bit under
3 GB and looks great on WD set top box. If you want to output SD .avi just add
a line to the .avs script to size down to 720,480. Very nice hidden gem!