I often get questions about how to deal with documents in document libraries. Can I use folders? how many documents can a library contain? or how to deal with bulk imports.
Blog.ekegren mentions an article on MSDN, about how to set up WSS as a collabortive file store. This article also talks about how to deal with document libraries and its limitations. Ekegren did a test importing a million items into a SharePoint list, so it’s worth reading his experiences. 
About the document library performance limitations:
Performance and Usability
To maintain optimum server performance and ease navigation of the document libraries and folder structures, use the following guidelines as the upper limits when organizing your files:
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1,000 files in a folder |
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1,000 folders per document library |
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1,000 document libraries per site |
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50 megabytes (MB) per file |
When a site is maintained within these parameters, typical throughput is as follows:
read the complete article
Other usefull sources which I mentioned before: