lr-genesis-plus-gx and lr-picodrive have support for the CHD (V1-V5) archive format. This format will save space and allow you to keep your Mega CD/Sega CD ROM folder tidy. See Creating CHDs from ...
Simply execute the script with a single argument: the relative path to a Sega Genesis or Sega Mega Drive binary ROM file. The script will then execute and verify the checksums match. If they match ...