The main difference I have found is in driver stability.
I've had a fair amount of experience with Dell 1950/R410/R610 1U servers running RedHat, and we had such stability problems with an R610 running RHEL5 as a backup server/NFS client (Isilon NFS Server) that we decided to stop using the onboard Broadcom PHYs and installed Intel PCIe Dual GigE NICs. It only failed under heavy load, but it did fail. Another 1950 with Broadcom PHYs also had stability problems under heavy NFS load.
RedHat later fixed the R610 problem by issuing new Broadcom drivers, but by that point I no longer had any confidence in the Broadcom drivers. Even after getting the updated drivers, we got slightly better throughput from the Intel GigE interfaces. (We were not, however, using TOE.)
If you know which OS you're going to use, I strongly recommend searching your OS's support site for Broadcom related driver issues before you settle on them.