Seems like the Mac OS X API, like the Skype app itself, lags a little behind the Windows/Linux versions and the Applescript interface (which is easiest to use from a cgi script) is only partially implemented.
I did manage to get a simple web-based IM sending app running on OS X server. Try this form to Skype and I’ll post your message here as a comment:
This obviously only works if I’m online too. Seems to get queued in the Skype cloud even if I’m not.
(I’m not providing a generic web to Skype gateway here, for that try InstantSkype.)
Update: see my Skype forum post on why managing calls with the Applescript interface is a problem.