Copy everything off your Micro SD, format it, and copy them back on one by one in the order you want them to show up.
Thanks for those links!There is no need for format/copy games off and back to the card. Gateway lists games in order they are listed in the file allocation table of the microsd, ie in the order in which they were copied to the card.
There are tools that will re-order them for you, for times when the application itself does not provide sorting:
Sort alphabetically: http://www.maxconsole.com/maxcon_forums/threads/283015-Gateway-3ds-SD-Manager-v1-0-release
Custom Sort: http://www.maxconsole.com/maxcon_forums/threads/282131-Gateway-3ds-Rom-Sorter-beta
Thanks for those links!
Thats even better the severe OCD in me thanks you haha.I meant to update the 'custom sort' URL but accidentally replaced the aphabetical one. Should be:
Sort alphabetically: http://fat-sorter.software.informer.com/download/
Custom Sort: http://www.maxconsole.com/maxcon_forums/threads/283015-Gateway-3ds-SD-Manager-v1-0-release
I've only ever used the first one as I just wanted to put newly added games into alphabetical order.
Thats even better the severe OCD in me thanks you haha.
edit
hmmm i just get redirected when I try to download that alphabetizing software