MSDN - Choose between ASP.NET 2.0 Web Parts and Windows SharePoint Services 3.0 Web Parts
You must create ASP.NET 2.0 Web Parts when you can. However, there are a few exceptions when using SharePoint-based web parts can provide benefits. The following table shows the decision matrix to help you choose the best option based on your business needs.
Create a custom ASP.NET 2.0 Web Part
For most business needs.
Distributing your web part to sites that run ASP.NET 2.0 or SharePoint sites.
If you want to reuse one or more Web Parts created for ASP.NET 2.0 sites on SharePoint sites.
To use the provided data or functionality of Windows SharePoint Services 3.0. For example, you create a Part website that works with a website or data list.
Create a SharePoint Web Part
If you want to migrate a set of Web sites Parts that use SharePoint sites Part of the infrastructure for Windows SharePoint Services 3.0.
To create cross-page links.
To create connections between Web Parts that are outside the Web Part zone.
To work with client connections (Web Part Page Service Component).
To use a data caching infrastructure that allows you to cache the contents of a database.
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