Joel Oleson (a member of the MS SharePoint Products and Technologies Team) wrote earlier this year on whether the file server is dead or not. A lot of the points he makes about what should and shouldn’t be stored on SharePoint servers are fairly obvious – don’t do application or hotfix rollouts using SharePoint, for example – but some of them were a bit surprising or at least worth mentioning.

• Storing SQL databases as a SharePoint object doesn’t really make sense; linking these in via the Business Data Catalog functionality does.
• Just because Access 2007 files can be stored in SharePoint doesn’t mean they should be stored in SharePoint. This depends largely on the complexity of the database and how it’s used.
• Direct quote: “Access 2003 databases should not be stored in SharePoint document libraries where multiple users need to edit the access database simultaneously.”
• SharePoint is not developer source control, though the terminology and functionality is roughly the same.
• If Excel spreadsheets have data that cross different spreadsheets, this may cause issues due to how file paths are encoded when those dependencies are created.
• File storage: cheap. SharePoint storage: expensive relative to the cost of file storage (since almost everything’s stored in a database).
• Basically, if it’s a collaborative file share, SharePoint can replace it. However, if it’s simply file storage, this may not be cost-effective.

Joel has a follow-up post here – some further bullets:

• Having users completely copy over all their private documents into My Sites or Team Sites isn’t what you want to have happen.

There are plenty of others talking about the same subject (see the links Joel provides). This additional commentary isn’t bad.