This happens sometimes with me and so far I've just had to put up with it.
Sometimes it can be the FireWire port, sometimes it can be the OS.
I suggest that you use Drive Utility (In utils) and do a quick permission check and a scan for errors.
This fixed one of my drives in one case but yours may be different.
If all else fails, get something like Disk Warrior and do a complete fix.
Thanks. I've repaired permissions quite a few time already, with no change. Everything else shows up fine either USB or FW (floppy, CDs, ipod, flash memory...). Nothing systematic.
But I'll give Disk Utility a go.
I hope others will also find the answer to this trivial question useful so here it is....
activate the finder (click on desktop)
go to Preferences
first options relate to what is shown on the desktop: click Hard drive for external HD to show up!