I was wondering if a function could be made that would cause a window to ignore mouse-clicks (unless a modifier like shift was held)

Also I would be interested in an 'Always on Bottom' function. This seems fairly straight forward given the code for the 'always on top' and 'send window to back' functions (however I dot have access to that)

Ah that's fine, thanks for the response;

I've somewhat solved the click-through with rainmeter (by creating a full-screen window with 99.9% transparency that sits just above the window pushed to the back, it absorbs all clicks (but never comes to the foreground, Not perfect, but it works)

Alternatively;
Is there a way to detect when a specific window looses focus? Then automatically run the send to back function on it?
Or is my only option creating a function that runs every .5 seconds and checks?

Great, I was going to suggest this actually Heres a list of some of the potential triggers you could include:

On different mouse/keyboard usage (I have my living room hooked to my rooms pc, so when I watch movies I have to disable the 2nd monitor via hotkey currently)

On Shutdown/sign out/sleep/hibernate
on wake/unlock/Startup
On run/end of X program
On Window minimize/maximize/close/activation/deactivation
On custom function completion.
On Inactivity (no mouse/keyboard/audio for 60? seconds, the audio check is just to make sure they aren't watching a video or something and there might be a better way to check)

On Specific drive insertion (this would be nice, to backup a specific folder automatically just by attaching a specific flash drive)

Awsome, off hand, heres a few:
Video playback (detect the playback of a video file, preferably in-browsers too) This way you can enable/run specific functions (maybe enable some special play/pause hotkeys)
DirectX (or some other way to detect a non-specific game has started/stopped)
New monitor detected
New drive detected (I would imagine people might like to set certain data to backup automatically, or something of the sort, to an external flashdrive