1) Given a system running FreeBSD 9.1-RELEASE, is anything bad gonna happen if I insert a drive into this thing while the system is running?
Assuming your board supports sata hotswap (too lazy to check) it'll be just fine. I've done this many times with the machine I'm messing with zfs on.
Will I be able to mount partitions contained on the drive in question after I do so?
y
2) Given a system running FreeBSD 9.1-RELEASE, is anything bad gonna happen if I remove a drive from this thing while the system is running, assuming that I have already properly umounted all relevant partitions first?
No. On my test machine I've been yoinking drives without even any unmounting and it's just fine (up until I pull that last drive in my array and zfs shits the bed).
Honestly, the only thing you have to worry about is if you're in there messing with cable ends that you don't accidentally touch the cable clip to something else on the board and short it out.
3) Assuming that I want to do this stuff, what BIOS options should I be setting or unsetting on the motherboard?
You need the sata ports running in straight up pure ahci mode (as opposed to "IDE mode" or "compatible" or something that emulates old style parallel-ata). Be aware that Windows up through XP doesn't support ahci, so if you're dual booting an old system you'll have problems. You'll also almost certainly want to disable any motherboard-based raid options too, as they tend to be complete crap.
sata vs esata
esata is pin-identical to normal sata. The only difference is that esata has a more robust plug design meant to handle frequent [dis]connections and tighter electrical requirements in the cable for longer distances. As far as your board/OS is concerned, it's just another sata port.
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