One thing I've had a problem with is that although sometimes I like to play 1.5.2 or other older versions of minecraft, I currently have to manually swap out my mod setups for each version. I got an error loading 1.6.1 about conflicting mods when having both the 1.5.2 version and the 1.6.1 version of Rei's Minimap in my mods folder.
My idea is to make the mods folder per-profile, so that I can have my 1.5.2 mods with my 1.5.2 installation, and my 1.6.1 mods with my 1.6.1 install, no switching needed.
I really hope this is something possible to do, and I'm grateful for all the hard work the Forge team puts into getting Forge to work with each update.