One of the most frustrating aspects of an iOS device is the way it's joined at the hip to a single iTunes library. This isn't a huge deal with content you've bought from the iTunes store (which you may re-download), but with content you've added yourself... grrr. Enter SuperSync, a program that allows you to sync multiple libraries so you can upload any of your content to any of your iOS devices. It costs £15 for two computers, or £17.50 for five, or £21 for ten computers. See all Audio and music software reviews.
SuperSync works with iTunes, directly working with the iTunes library. In fact, the program looks quite a bit like iTunes with a three-paned interface. What SuperSync does is load your local and remote libraries (from multiple iOS devices, network libraries, remote PCs, etc.) and synchronize files between them, so every library now has every file. With all of your files now held the iTunes library, you can easily sync everything to your device. It can also backup and recover music to or from your iPod, iPhone or iPad. There's a Mac version as well. See Group test: what's the best audio/music software?
SuperSync also has other features lacking in iTunes such as duplicate file reporting and removal, missing track reporting, etc. that are very helpful in managing a large catalog of music from various sources. It interfaces with iCloud, and will even analyze and repair corrupted libraries. Take a look at TuneUp 2.4 review.
My only minor gripe with SuperSync is that the help is only available at the Web site, and not within the program. Using a "help" menu or question mark, instead of referring to it as online documentation under the tools menu might make it a tad easier to spot. You'll need the help —SuperSync is powerful, but not simple, and the language is a bit technical when you get into the more complex features.
All that said, SuperSync is super handy for those of us that have multiple iOS devices and libraries. With it, you no longer need fear the "All existing files will be replaced" iTunes messages.