Strange how i've only just signed up because of trying out LaunchBox. But looking around it seems I should have joined a long long time ago...
Have been emulating a while before using Mala, currently comparing mGalaxy (like it) vs new install of LaunchBox (lets see this baby!). Used RetroArch from the beginning but it's still not the perfect solution, eg. Amiga support is really bad :( .
Also spend my nights working out my folder structure! I used to have seperate Roms folder, Emus had the bios,images etc. But now I figure its best to keep resources (roms,saves,bios etc) separate from Emu's, in Console folders. And leave Emu's just to them selves.
Currently have evolved to (using N64 as example):
Emulation > Consoles > Nintendo - N64 > Roms / Saves / Screenshots
Emulation > Emulators > Project64 2.3
Emulation > Emulators Frontend > mGalaxy / LaunchBox / RetroArch
I'll probably change it all back again once I get round to re-sorting MAME! grrr but :)