What is difference in developing applications using .Net Framework, Asp.net and developing application in Sharepoint (MOSS or WSS)?
I highly recommend checking out this thread for various pain points:
https://stackoverflow.com/questions/256407
Since SharePoint is built on ASP.NET, the argument can be made that anything you can do with ASP.NET you can do with SharePoint but the reality is developing applications for SharePoint is not for the faint-hearted and you should expect a much longer development cycle, particularly if you are new to the platform. I suggest becoming very familiar with Google, StackOverflow, and .NET Reflector because a lot of what you need to know is not in the documentation or hard to find.
It's not all bad though. You get a lot of infrastructure out of the box like authentication, versioning of data (if you are storing your data in lists), and incoming/outgoing email connectivity to name a few.