For batch cropping, simply press B to go to the Batch Conversion screen. First you choose which file to add to the batch job, but for the cropping you have to go the Batch Conversion Settings, check "Use Advanced Options" and then press the "Set Advanced Options".
You'll be presented with a bunch of different transformations to choose from, the first of which is the Crop options.
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Current projects: Bucky O'Hare (NES), Metal Storm (NES), Clock Tower (SNES), Ristar-The Shooting Star (Gen), Sonic The Hedgehog (Gen), Sonic CD (Sega CD), Mega Man Zero (GBA), Battletoads (NES)