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Firefox searches a number of locations for plugins, one among them is in the user's Mozilla settings folder. This MozillaZone knowledge base article describes the process of finding the path for the user plugins folder quite well. It also turned out that the user-level plugins folder is not profile-specific ... thus you cannot have a profile with one set of plugins and another profile with another set of plugins. In case of linux (I tested with Ubuntu in particular) the user plugins folder should be at $HOME/.mozilla/plugins. The folder does not exist by default, you've to create it for yourself.

One more thing: if you've two different versions of the same plugin (one in the system plugin folder(s) and one in the user plugins folder), then unfortunately only the system-level plugin will be loaded. Firefox searches first in the system-level plugins folder and afterwards in the user plugins folder. If it finds a plugin that is already loaded, then it won't load it again (from the other location). This means that you cannot have the normal Adobe FlashPlayer plugin installed and have a debug version in your own plugins folder, because Firefox will load the system-wide installed, normal version. Quite annoying imho.