Here are some of Advantages/Disadvantages of SharePoint apps over ASP.Net apps:
1. Many built-in features are available with MOSS which can be used to easily develop complex solutions.
2. Rich Security features which come built in.
3. Integrated with Content Management.
4. Very less efforts required to create basic sites with lot of features.
5. It is quite scalable.
6. OOB Integration with Office products.
7. Rich backup techniques
8. Business process can be integrated with Workflows.
9. Multiple sites can be created with the help of templates.
1. It is difficult to add custom code in SharePoint. Features and WSP files take time.
2. Difficult to solve the problems in development.
3. Creating ASP.net pages is easy then creating web parts.
4. Cost is very high.
5. Performance for ASP.NET apps is much better.
6. Very few experts are there.
Advantages/Disadvantages of ASP.Net apps over SharePoint apps:
1. Here we have lot of control on application in terms of DB, UI.
2. Less cost to build.
3. Easy to develop and deploy.
4. Plenty of resources.
1. Takes lot more time to get same functionality as of SharePoint.
2. There is nothing built in. So every solution needs to start from zero.
3. Good DB knowledge is also required to create sites having data.
4. Security needs to build.