Halley, I had definitely been considering doing a modular system. Good call on the mastermind arduino, I didn't think of that one... Perhaps that mastermind can be the communication protocol between PC and the subsystems.
Retrolefty, I agree with you regarding the selection of the sensors. I know my way around a circuit board/saudering/general electric work, however I don't know much about sensors themselves. I was researching a way to monitor temperature and humidity, and I thought I saw hydrometers that would do both, but I didn't really reach a conclusive answer. I'm hoping to address these specific issues in the Interfacing forum. Also, good call on the audible buzzer -- definitely didn't think of that one, and i'm sure it will shave off frustrating debugging time.
Thank you so much for your input so far. I'm going to hit the whiteboard again and perhaps post a sketch of the systems.
PS: I'm an open source advocate, so I'm going to draw everything up, document the process, and publish my designs/code/etc under GPL/BSD. I also plan on making an instructable. Any tips for linux-friendly graphing/circuit design would be welcome!