I usually set up my bios to boot floppy 1st, cd 2nd and hdd 3rd. It may take a few seconds longer to boot up but its worth knowing you can use any of your devicess to boot without messing with your bios.
I agree, the 3rd party apps should be kept and the most important thing is to keep your system well maintained. 10 minutes a week is really all it takes.
I updated my system today. Followed Cherokee chiefs checklist from the G$TTV forums and had no problems, although now my pc will probably explode in flames having said that. I don't notice any sped difference.