It's already underclocked. It's a Celeron E3200 and it's running at 1.2GHz and heavily undervolted, but even so, I don't want it "on" when for 60% of the time it's not actually doing anything, especially as the LSI RAID card seems to lack provision for spinning the drives down.
I've pulled the ethernet cable as soon as it goes into sleep as you suggest. In fact, I've pulled it, rebooted, and then put it to sleep. There are no issues when there is no network cable attached, which makes me assume that it is not an issue with the server's hardware, with the Vista install, or the BIOS. The BIOS has very few settings for WOL anyway.
I've attached my DSL modem directly to my server just to see if having ANY network device attached causes this wake from S3 issue, but it stayed soundly asleep.
As soon as I connect it to the router, despite nothing else being connected to the router, it starts waking up 30 seconds after being put to sleep. This router is broadcasting something... anyone got any ideas what it could be? As stated earlier, DHCP is off.
Mouse and keyboard wake is disabled in the server's BIOS.. so that rules that out.
Does anyone from D-Link read these forums?