I know this is a VERY late reply but I thought I should update this with the success I've had.
Using psexec as suggested by derkaderka, I've been able to successfully put my file server into standby using the below:
psexec \\server -s -d Rundll32 Powrprof.dll,SetSuspendState
With this setup I'm now able to put both my desktop and file server into standby so they start up much quicker than a standard 'cold boot', plus wake on lan works like a charm everytime without fail.
My previous experiences with WOL have taught me that if your trying to wake up a PC either on a LAN or over the net that's been shutdown totally tends to be a bit hit and miss. For me, majority of the time it wouldn't work.
HOWEVER, waking up a PC from standby (I believe it's S3?) over a LAN or the net has worked 100% everytime. I simply use the WOL feature in the Tomato firmware on my Linksys WRT54GL, but I believe the Depicious WOL tool will also work from a remote location (you may need to either allow multicast or allow UDP port 9 through your router?)
Hope this is of some help to someone, and thanks to everyone who replied
