Randomly figured it out today.
Edit /etc/network/interfaces Add "post-up mii-tool -F 100baseTX-FD" to your particular 'iface' declaration. /etc/init.d/networking restart (just to test)
This isn't the most generic or clean ways of doing this but it is pretty reasonable. post-up apparently executes the passed command (could be a script) every time the interface is brought up so it could be useful for pppd stuff or firewall rules or whatever. If your NIC doesn't use the mii interface then you'll have to find a similar application to take care of it.
Anyways, since at least one other person was interested in this I figured I'd waste a few bits,