My friend Adam asked me recently about defrag.nsf. In case you don't know, this is a Windows-only tool for Domino that will do a file-level defragmentation of Domino databases. According to the product page the theory is this will increase performance. I haven't tried the product so I can't state whether this is true or not, but I do know that you can get the same results for free.
defrag.nsf is using the Windows defragmentation API to do file-specific defragmentation. Microsoft baked this into Windows NT 4 and the same API has been in Windows 2000, XP and Server 2003 and 2008. It is robust, stable, and has been proven over time. Because all the necessary libraries are included with Windows you could write this application yourself if you wanted to.
But you don't have to. Sysinternals, a division of Microsoft, has the free contig tool that does the exact same thing. You can defrag a single file, a directory, or recurse directories. And it accepts wildcards, so you could defrag "c:\program files\ibm\lotus\domino\data\mail\*.nsf".
If you decide you want to find out if file fragmentation is an issue for your Domino server it wouldn't hurt to try out the free contig tool and compare it to the results from defrag.nsf.
P.S. While I was researching this I came across Ulrich Kraus' write up of contig. The comments there include links to more free defragmentation utilities.