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I’ve been researching the reasons for not moving everything from your shared drives to SharePoint. These seemed to be the common factors mentioned (with varying levels of explanation/justification):

1. Storage costs
“SQL Server storage is more expensive and complicated than network storage” -objectmix.com

2. Archives
“The basic collaborative nature of  Sharepoint probably doesn’t support long term historical archives of data.” -objectmix.com

3. Security

4. Backup and restore issues

5. Types of files
File types not to store in SharePoint: scripts, executables, multi files, CIFS links, some access databases, Outlook Personal Folders, Application files (*.exe, *.dll, *.bat, *.log, etc.), large backup files (> 50 MB *.zip, *.iso, *.bak, etc.),DVD images (*.ifo, *.vob).

6. File usage
Usage reasons not to store in SharePoint: files not accessed for months and files without collaborative value

7. Size of files
File size restrictions seems to be the most commonly mentioned point, with most sources suggesting an upper limit of 50-100MB per file.

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:

 o   1,000 files in a folder

o   1,000 folders per Document Library

o   1,000 document libraries per site

o   50 megabytes (MB) per file”

– tributarysoft.wordpress.com

8. Linked documents
“Linked documents and files cannot be run from a SharePoint site, as the dependency on an external sources isn’t captured in SharePoint.”
– blogs.msdn.com/joelo/

9. Only in SharePoint for search purposes
The files in the drives can still be searched for in SharePoint. “Just index them with Microsoft Office SharePoint Server and they will become discoverable as well.”
– jopx.blogspot.com/

Sources:
http://objectmix.com/sharepoint/337243-sharepoint-replace-network-shared-drives.html
http://blogs.msdn.com/joelo/archive/2007/11/08/what-not-to-store-in-sharepoint.aspx
http://tributarysoft.wordpress.com/2008/08/18/windows-file-share-migration-to-sharepoint-nyc/
http://blogs.msdn.com/mikewat/archive/2006/12/09/file-shares-vs-sharepoint.aspx
http://jopx.blogspot.com/2007/01/sharepoint-document-libraries-or-is.html