Store Files in SQL Server or keep them on the File Server?

Question

Currently we have thousands of Microsoft Word files, Excel files, PDF\'s, images etc stored in folders/sub folders. These are generated by an application on a regular basis

Answer 1

Rather than writing a custom DMS (document management system), you should probably consider buying one or using WSS / SharePoint as this will handle all the mundane details (storage, indexing, meta-data) and let you build your custom functionality on top.