I am writing a web application in ASP.NET 3.5 that takes care of some basic data entry scenarios. There is also a component to the application that needs to continuously po
You might find that the SQL Server job scheduler sufficient for what you want.
I'd go for the separate Windows service primarily for the reasons you give:
I'd also add that it could well have some impact on the performance of the web site itself - something you want to avoid.
The buzz-word here is "separation of concerns". The web site is concerned with presenting the data to the user, the service with checking the integrity of the data.
You can also update the web site and service independently of each other should you need to.
I was going to suggest that you look at a scheduled task and let Windows control when the process runs, but I re-read your question and noted that you wanted the checks to run every couple of minutes. The overhead of starting the process might be too great in this case - though some experimentation would probably prove this one way or the other.
If you use a scheduled task there's also the possibility that you could start the next check before the current one has finished - something you can code for if you're in complete control.
Why not just use a console app that has no ui? Can do all that the windows service can and is much easier to debug and maintain. I would not do a windows service unless you absolutely have to.
Console application does not do well in this case. I wrote a TAPI application which has to stay in the background and intercept incoming calls. But it did it only once because the tapi manager got GCed and was never available for the second incoming call.