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Is it a good thing to build everything in the existing gui of sharepoint or is it beter to create a custom website and use sharepoint as a backend?

how can I make that decision?

I think that just customizing the master pages would work, what do you think?

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I strongly recommend against creating custom UI if you don't have really strong requirements toward that. Upgrading might be big task when the time comes and in the end you might end up being forced to implement lots of OOB SharePoint functionalities in your custom app.

If custom Master page(s) is enough I would consider going that path instead.

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Wouldn't this be more of a requirements decision based on the needs of the business. Also, what version of SharePoint are you using? I ask this question because to customize WSS 3 or Foundations is a little more tedious to brand. The full licenses provide a set of layouts adn master Pages that can get you started easier to develop a customer facing custom portal. With the publishing features you can use some useful web parts like the content query web part to roll up data etc.

No doubt that SharePoint can be the back end and front end of a great publishing sites. Checkout this site for demos

In the end, evaluate the requirements and than come back to the question on what approach should be taken.

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