The Power User's Guide to Video Encoding with Handbrake
How to Back Up and Transfer Custom Profiles
The custom settings we laid out will get you off to a good start, but to truly take advantage of Handbrake, you'll want to spend some time fine tuning the app based on your specific needs. Finding the ideal balance of quality to performance is going to take some trial and error, and you could spend hours experimenting and setting up different profiles for all your (and your family's) mobile gadgets. So the last thing you want to do following a catastrophic system crash or hardware upgrade is go through the process all over again.
Handbrake saves your custom settings to the hard drive, but it's not particularly easy to find, nor can you back them up through the GUI. Before you begin, you'll need to configure Windows to show hidden files and folders. To do this, open up your hard drive, press the Alt key, and navigate to Tools>Folder Options. Click on the View tab and check the Show hidden files, folders, or drives radio button. Press Apply.

You'll find your custom settings nestled away in C:\Users\[USERNAME]\AppData\Roaming\Handbrake. See the user_presets.xml file? That contains all of your custom profiles you created. Copy this to a USB stick or other place for safe keeping, and transfer it back to the directory on a new build or install.
Queue It Up (even from Multiple Optical Drives)
Far be it for us to chastise anyone for sitting in front of a computer all day, but it's a little different when you're talking about an all-night gaming session versus waiting for Handbrake to finish encoding a video so you can fire up another one. Nobody in their right mind is going to do that, nor does Handbrake expect you to.

Instead, add several jobs to Handbrake's Encode Queue and let the program do its thing while you sleep the night away or while you're off toiling for the man. After you've configured a video file for Handbrake to encode, press the Add to Queue button instead of Start. Once you do that, click the Source button and pluck another video, press Add to Queue again, and rinse and repeat for as many videos as you need to encode. To view your queue, just click the Show Queue button, where you can also prioritize rips by moving them up or down. When you're ready to start encoding, hit the Encode button in the Queue window.
If you own multiple DVD drives (and who doesn't?), you can have Handbrake queue up rips from each one, but it gets a little tricky. For the first DVD, choose the appropriate DVD drive as you normally would, choose a Preset, and click Add to Queue. Logic would dictate that you simply repeat this step for each of your other optical drives, but often times this will trip up Handbrake and it will end up scanning the second (and subsequent) drive indefinitely.

To prevent this from happening, for each additional DVD drive/disc, choose DVD/VIDEO_TS Folder from the Source menu and navigate to your DVD's VIDEO_TS folder. Before adding it to the queue, be sure to edit the file name in the Destination field because using this method doesn't retain the DVD title.
Serve Up Soft Subtitles
What's that you say, it's not possible to tack on soft subtitles with Handbrake? While that was true for the longest time, version 0.9.4 addresses this glaring oversight and Handbrake now lets you include soft subs rather than permanently hardcode them onto the video track. Not only that, but you're free to add multiple subtitles too.

That's all well and good, but what if you have a collection of downloaded videos without subtitles? As luck would have it, there are several websites dedicated to serving up nothing but subs, some of which include:

Adding a soft subtitle with Handbrake is pretty easy, but follow closely. To start with, click on the Subtitles tab in the main window. Mash the Import SRT button and find the .srt file you downloaded (or that you already have) and click Open. You should now see the .srt file in the Track pull-down menu, but just because you imported it into Handbrake doesn't mean it was added to your video. Highlight the .srt file from the pull-down menu and punch the Add button.
To add multiple subtitle tracks to a single video, repeat the above instructions, and make sure you add each one by pressing the button, not just importing. If you want one of the tracks to come up as the default, check the Default box before adding it to your video.