Handbrake's SVN will address some of the VisualHub advantages in terms of fixing crashes. 0.9.3 is still a decent converter if you know the workarounds.
I've moved on from Handbrake. I spent all week trying to convert stuff. Crashed every time...
VisualHub 1.34 did the job first time perfectly.
I'm trying the filmredux alpha right now....
Chose AppleTV & "Keep Surround if possible," 720p mkv.... had to install extra binaries as noted in the readme. SO far so goods... Conversion just started. Will keep you posted.... Says 89 mins left....