Some time ago I wrote a blog post about fixing slow iTunes backup. The article became the by far most visited one on this blog and we are still getting tons of visitors from google every day. When reading the comments you can see that lots of users seem to have the same/similar problem.
The issue results from the fact, that some apps save lots of files to the file system of the iPod Touch, iPhone or iPad. While – of course – nothing speaks against using the file system to save data, the problem starts when files getting to many. iTunes then needs ages to copy them to the computer when doing a sync (the backup before the sync in particular).
If using a reasonable number of files you will never have a problem. However, if your app syncs data from the web (for instance a news or rss reader) make sure that you delete the read / no longer needed files. Please :)
PS: Personally, I haven’t worked on apps that make extensive use of the file system. If you have, feel free to share your experiences.