Yep, I've heard both Compaq and Dell have used ATX plugs with non-standard pinouts. As for HDD some makers put a very basic BIOS on the mobo and the rest on a special partition of the HDD. Usually you can find a floppy that will create it on a new HDD, but it's a pain. I haven't heard of any thing much past early P1s that did this, so anything using a 4GB+ HDD stock is probably safe.