My vote is for:
Allow Pause to work while the script is idle, at least if it has timers
PixelWaitColor: Waits for a pixel to change color (BeastMaster).
The ability to detect which part of a window (e.g. title bar or scroll bar) the mouse is hovering over so that hotkeys can be made more context sensitive.

----MbuttonTitleBar:: RbuttonMenuBar:: etc.
ProcessExists / ProcessClose / Priority, etc. (Payam and others)
A built-in command to trim whitespace (and perhaps any chars of choice) from the beginning and/or end of a variable, perhaps using style similar to the parsing loop.
Joystick: Support for prefix+suffix keys but all on joystick (no keyboard/mouse combinations since most people have both hands on the joystick anyway)?
:idea:----Most PC flight sims have dozens of keyboard commands (engine, radar, weapons, targeting etc, so one needs to have a hand on the keyboard most of the time. For me, a keyboard prefix ( <+joy1:: ) would be more useful than ( joy1 & joy2:: ). I have already remapped my joystick buttons (logitech drivers) to output keyboard keys, so this is not a priority for me anyway.
Improve the reliability of the Send command and perhaps MouseClick/Move