Can you name the common things (logical ones) between file system storage and RDBMS? For sure both stores user's and system's data. For historical reasons the engines are quite different but can they be brought closer with current level of technologies? Why not?! Microsoft has made an attempt with WinFS but this adventure threatened Windows Vista relesase and was dropped from Vista. This mean we won't see it in Windows Server 2008 either as they share same core AFIAK.
But still we can have small good even now - transactions in file system or trade name - Transactional NTFS (TxF)
There is a good article explaining TxF in July 2007 issue of MSDN Magazine.
The easiest use of TxF is with native code. Being .NET developer this isn't that good for me but in the article's sample code is placed a basic wrapper you could start with.
If you're interested but too lazy to read take a look at Channel9 screencast Developer, Meet Server #1 - Transactional NTFS