This is a hotly debated issue. You can look around and find lots of tests and research on the subject...
However, the card itself will be able to negotiate a full 1GB network connection just fine. The PCI bus doesn't have anything to do with the network negotiation, but has everything to do with whether it can feed the card (or pull incoming data off of the card) fast enough to use the bandwidth available to the card.
The net is that you'll get more real throughput than 100MB, but depending on your specific hardware, you may not get enough to make it worthwhile. It could be 125MB, it could be 200MB, it could be a bit more.
One thing I recall seeing is the statement that large file transfers are much more efficient on the PCI bus than small files. Evientally, the reason is the overhead on the PCI bus regarding processing the transfer. All that is way above me...
I'd call the manufacturer and ask them if they have any data they can share with you about GigE NICs on your particular board. If it is a really bad board, you may not even be able to get full performance from 100MB NICs that you have right now...
One last thing to think about is "Teaming NICs" or NICs that support Cisco's EtherChannel. Network Magazine or Network World had a big article on this. You may be able to get more performance from this type setup than you would from a GigE NIC.
