The latest build of HotkeyNet has new commands for adjusting the position and size of a window:

setwinpos
setwinsize

Here's an example that changes the position of a window called "Ubertastic" to screen location x = 200, y = 100:

Code:
<setwinpos Ubertastic 200 100>
And here's an example that changes the size of that same window to 800 pixels across and 600 pixels vertically:

Code:
<setwinsize Ubertastic 800 600>