Here are two Mac utilities that defragment the iPod:
PodLock by Micromat
http://micromat.com/podlock/podlock_introduction.html
and TuneTech by ProSoft
http://prosofteng.com/products/tunetech_info.php?PHPSESSID=6fff8b8a82a718dcbebd0 af906405f52
(Both of these do other things as well.)
I did a search at Apple support for 'defragment iPod' and came up with this, which addresses a Windows-specific problem:
http://docs.info.apple.com/article.html?artnum=300554
It says that when you do a 'restore', it defragments the hard drive. So apparently there's nothing inherently damaging about defragmenting an iPod.
I have Micromat's Tech Tool Pro 4. It sees the iPod, and says it's available for testing and repair. (I just got my iPod a few days ago, so have no need to run the tests yet. If I encounter any problems down the road, I'll post them.)
So if you already have a 3d-party utility that does defragmentation and optimization, you might check and see.
Those other utilities have other functions (e.g., backup and restore), at least some of which are available elsewhere (like from shareware or freeware). They might still be convenient because they have all the functionality in one place, but for now I think I'll use Tech Tool.
Apple, how about a statement about maintaining the iPod?