Trimming roms comes in one of two forms:
00/FF stripping: rom chips come in sizes of 2,4,8,16,32,64..... and naturally your code does not have to be that size. To make up the space 00 or FF values (or occasionally alternating 00FF00FF type things) are added to the end of the code, these can be safely stripped on nearly all occasions (00 of FF is occasionally used to end a sequence of text or something and by deleting it you can cause issues, giving a few back sorts said issues).
All EZ software does it but GBATA can be used too: http://www.gbadat.altervista.org/tools.htm
The second kind of rom trimming is pretty much a DS only affair (only the famicom disk system is the other one here), to explain it we have a nice long thread containing pretty much everything you will want to know:
http://ezflash.sosuke.com/viewtopic.php?t=457 In simple terms it involves breaking apart the rom and putting it back together with less/smaller files, the prime example would be something like castlevania where by removing the intro movie you effectively halve the rom in size.
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