I know that in MAME some good roms sometimes use files from clones to work correctly.
Like Octopus said, delete away for console games.
Also (mainly for newb's reading this thread), you probably have the above backwards -
If using split sets (the most common setup), all parent games will normally work fine without any of the clone roms, however, clone roms will probably not work if the parent rom is deleted.
Ways to sort ROMS -
Split sets - Parent games contain all the roms required. Clone games contain only the Roms that are unique from the parent set. This is the most common setup, b/c it saves a ton of hd space - Example - I will have roms for 1941 and 1941j, but my 1941j rom will be less than half the size of my 1941 file, b/c many of the roms it needs are in 1941.zip.
Not Merged sets - All files contain all the roms required. This is rarely used because it uses a lot of storage space. The only advantage is that any rom can be safely deleted - Example - I will have roms for 1941 and 1941j of roughly equivalent size, but deleting either rom won't affect the other game.
Merged Sets - All parent and clone roms are contained it the same file. Example - I will only have a 1941 rom, but it will play both 1941 and 1941j. This provides slightly more HD storage savings than the split roms method, but is rarely used, primarily b/c if a later MAME rev adds 1941b, I have no way of looking in my rom directory and knowing if my 1941 rom supports it or not.
BTW, ClrMAME can generally convert between any of the methods.