Maximum PC has an article saying you can do this.
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.