Having the same issues with my late '09 mini. In the beginning I got 1Gbit/s links with no problems. Then after about 12 months the Mini started playing up.
Same pattern as described in the other posts - other machines connect just fine at 1Gbit/s.
Mini -> Netgear GS605 switch -> Linksys WRT54 router.
also tried
Mini -> DLink GB switch -> Linksys WRT54 router
So today I tried re-crimping my cable to cross-over, and when inserted into the mini, the Network Utility would show the Link Speed switching between "1 Gbit/s" and "inactive" before finally settling on 100Mbit/s. This is with automatic hardware settings.
Forcing a manual 1000baseT hardware setting switched between "not connected", "unknown state" and "Connected", before finally settling on 1 Gbit/s.
With the cross-over cable and the mini reporting a 1 Gbit/s link however, I get:
Internet speed has dropped from 16mbit to about 1.5mbit.
LAN performance is rediculously slow
Recv. Errors are piling up very fast (Network Utility)
So even though it seems like a 1 Gbit/s link, there are issues.
Back to the regular cable and 100Mbit.
*sigh*
Side note: first saw the issues in Snow Leopard. Upgrade to Lion did not help.