This one's a bit mean, but still fun...
if the hand set of the phone on her desk can be taken apart put a small piece of lunch meat in the talking part of the handset. In a few days / weeks it will spoil and every time she picks up the phone it will stink horribly bad. Trust me this one works.
If she has a cloth seat on her chair you can pour water over it all (you have to get every part wet so the color looks uniform), then she sits down...
If she walks away from her computer you can change the language settings for just google to Klingon, or Yiddish or something.
In M$ Word you can change the autocorrect for words like "the" to funny, or evil things.
In the control panel you can invert the mouse movements and buttons.
Replace all her pens with caps super glued on
here's some more ideas:
http://lifehacker.com/373817/top-10-harmless-geek-pranks