Cropping black bars off of a video — Handbrake does this easily. Go to Dimensions [tab] > Cropping = "Custom", and tweak the left/top/right/bottom values.
Using the 'Preview' button before 'Start Encode' button can save you a lot of time, and allow you to quickly guess-and-check.
The left/top/right/bottom values aren't absolute pixel positions, rather they're relative to that edge. They're how many pixels you want removed from that edge.
Pro-tip: You don't have to guess how thick the bars are. Use VLC to save a frame, then open this still image in some image editor. If using Gimp, choose the Select Rectangle tool, and look at the bottom status bar while you're still selecting.