Finally used bioclipse for a real purpose, and to good effect, too:
what this shows (the images do get larger if you click on them! :) is the following basic workflow:
1) Exploring manager functions in the js console (bottom).
2) Writing a script in the js editor (top left).
3) Running and getting feedback in the rhino console (far right).
4) Viewing the results in the sdf viewer (top right).
What I was doing was searching through an sdf file (C10H16_filtered.sdf) for all structures with a cyclohexane ring as a substructure, then writing those out to a file.
Probably could have been done 5 other ways, but, well, it was more fun this way.
Oh, and it is a gist here.