The title of this question might be a bit clumsily phrased, but here\'s the situation:
I have a .NET web project deployed on my server.
To me, your problem sounds a lot like the deployment problem SharePoint solves through their Timer service running in each WFE, stsadm enqueuing admin tasks, that service dequeuing and running them etc.
What I would do is to
Another approach: what about using the plain vanilla Windows Task Scheduler? Look here, you can easily enqueue tasks remotely for ex.