I am also looking for a (free) ASP.Net based file manager and just did a brief survey. I tried Bipin Joshi's "Web Site File Manager" (the binaryintellect one referenced by DKarter). While it works, I felt it is going to be difficult to customize, it is a web page while I really need a control, and it is a bit dated at this point.
I almost gave up hope when I stumbled on IZWebFileManager:
http://www.izwebfilemanager.com/demo/default.aspx
Moved here: https://github.com/manishma/IZWebFileManager
It is licensed under the GNU GPL and it took 5 minutes to get running. I downloaded the code, added the DLLs to my project, and then added the control to a page, and bam - I had a professional looking fully functional web based file manager.
<iz:FileManager ID="FileManager1" runat="server" Height="400" Width="600">
<RootDirectories>
<iz:RootDirectory DirectoryPath="~/Content" Text="Content Folder" />
</RootDirectories>
</iz:FileManager>