Hi,
I would consider multiple redundant detection. Yes, there is noise in IR, and ultra sonic has its problems, as does using motion sense with a camera, but used together you should be able to do it reliably. The idea of mechanical, magnetic / reed switches on doors and window also sounds very good.
There was a book posted here somewhere, on alarm systems. Just do a search of the board and you should be able to find it easy. Ah, perhaps not. I think it was called Intruder Alarm or something similar.
Regards,
Robert