i believe the system menu just shows them in order ( or maybe reverse order ) that the folders are created. There is no homebrew that allows you to re-order them. But if youre really brave, you can delete them all and re-install them in whatever order you want them to be displayed in ( or maybe the reverse of that ).
You could also get on nintendo's website and ask about it in their support forum. Theres a chance that somebody that actually has some pull will read your request and it may get included in a future system menu update. Seeing as how thev'ye not included anything useful in teh past few updates, i think theyre due for some feature that users will notice and appreciate.