This post is primarily focused on more advanced users. If you aren't familiar with Terminal stop reading and wait for the next stable release.
1) Where can I find 64bit VLC for Handbrake 64bit 0.9.4+?
You have two options for this.
A) You can use the HIGHLY UNSTABLE AND UNSUPPORTED VLC nightlies from Nightly Build of VLC.
These are builds of the upcoming 1.0.4 version which work well for me on Snow Leopard (10.6.2) when running as 64bit. Carefully read the nightlies page if you decide to try them.
B) You can use the VLC 1.0.2 from http://www.videolan.org/mirror-geo.php? ... ntel64.dmg or http://www.videolan.org/mirror-geo.php? ... -1.0.2.dmg
If you want to use VLC to play videos too, download the vlc-1.0.2.dmg file, install VLC into /Applications/, and use the following instructions to force it to run in 32bit mode. 64bit 1.0.2 has certain bugs which cause it to crash when running in 64bit mode.
Open Finder, navigate to Applications, right click on VLC, click Get Info, Click "Open in 32-bit mode", and close the window.
2) How do I fix slow opening MKV files?
Run the following command in Terminal:
sudo chmod a+w /usr/X11/var/cache/fontconfig
You can read more about the solution here.
3) How can I fix block video/stuttering playback?
The reasons for this can vary. Your Mac may not be powerful enough to play the video in VLC, but use the information here first.