The mods folder is, as most of you know, in the .minecraft folder. I suggest moving it into the folder of the version of minecraft that you want to mod. Even though it does seem strange, I do wish that I could have two separate Forge versions.
If I am unclear, this is what I mean...
Say you want to load a Shaders mod in a version separate from one you use for normal, gameplay-changing mods (Such as ComputerCraft, or ThaumCraft). You would put your Shaders mod into .minecraft\versions\<version/filename>\mods instead of .minecraft\mods.
This would allow you to happily play Minecraft with shaders, but without the mods.
