As a casual user not a professional or heavy user, I loved handbrake as was among the best I used so far. I recently tested XMedia Recode 3.1.3.0 and quite impress with it so far. Couple of things to say about difference I found between latest XMedia Recode and nightly build HandBrake svn 5026.

For a 350mb avi movie using same settings for both encoders, XMedia Recode took just 7 mins to get it into 160mb mkv while handbrake took 15 mins to get to 155mb. But there is slight quality difference, handbrake uses Constant Quality RF 22.5 while XMedia Recode needs Constant Quality RF 25 to achieve the target filesize I wanted that was 150-160mb range. If based on target filesize Handbrake has superior quality but if based on encode speed XMedia Recode is way faster.

Pro
Faster encoding than Handbrake
Con
Bigger filesize than Handbrake

There seems to be a small mix-up with .wma audio. When you choose WMA codec v7 (wma1) it converts into WMA codec v8 (wma2) and vice versa.

Be careful installing the newest version 3.0.4.6.
Norton Security had an alert: one of the integrated DLLs (libfaad.dll) is containing malware (Suspicious.Cloud.7.F)
You should check by your virus-scan before installing - maybe, it is only a FALSE alert.