I have confirmed one widely reported workaround, and it's likely to be more palatable to programmers and sysadmins than it is to the general public. This workaround was tested with iPhoneOS 3.1.2 and iTunes 9.0.2 on OS X.
First, it's worth stating for the record that I polled two fruit company employees who worked on the iPhone, and both of them had assumed that the iPhone works like an iPod, and that iTunes supports the manual management of media from multiple source computers. Neither of them realized that the iTunes team had conspired to salt their application with nannyware, preventing people from peering with two media sources -- people like my unfortunate user.
Sadly, as I reported early, testing proves that two distinct iTunes libraries refuse to peer with the same iPhone through authorized channels. To establish a new peering relationship, you must allow iTunes to wipe the slate. This has been confirmed through extensive testing.
Now, some people insist that they can do this anyway, and I think I know why. Under certain conditions, you can copy your iTunes Library from one computer to another and it will retain its iTunes Library Persistent ID, which is a sort of globally quasi-unique identifier that tells your iPhone which computer it's peering with.
In fact, changing this Library Persistent ID is the key to hacking the nanny. The procedure is detailed in an article cited earlier in this thread. If you edit the iTunes Library Persistent ID on all of your source computers so that they're all valid and they all match, and if you then enable "manual" media management mode on your iPhone in iTunes, then you can drag and drop files and playlists onto the phone from any of your sources. Personally, I just set all my computers to have the same LPID. Don't forget to edit the LPID in both places: the "iTunes Music Library.xml" plist as well as the "iTunes Library" binary itself. Use HexEdit from SourceForge, in an equivalent too, to do this. (The procedure is well documented elsewhere. If it sounds nasty, rest assured it takes five minutes.)
This solves the mystery of those users who purport to have no problems managing their iPhone from multiple computers. They presumably copied their library files at some time from one computer to another, and I've seen a few ways to do this while preserving your LPID.
Of course, every medication has its side effects, and this is sure to have some weird ones. Here's one bizarre scenario, with a solution, an example that shows how the iTunes group has perverted traditions of helpful user interface design at the fruit company:
If you plug an iPhone containing DRM paid content into one of the libraries you fixed, but that computer is not currently authorized for your phone's paid content, don't click 'sync'. If under these conditions you then click 'sync', then iTunes will emit a warning insisting that you either "transfer" your paid content to this computer or suffer its deletion! The warning does not say what a "transfer" might entail, leaving the poor user to choose between a frying pan and the fire. The sneaky folks at the fruit company even went further: this dialogue has no cancel or close buttons! They make it look as if you must either submit to this unspecified "transfer" immediately or see your paid content trashed by a hungry iTunes.
Happily, there is a solution. Just pull the USB plug out of the back of the iPhone, and it will safely unmount without corruption. When this happens, iTunes politely closes its booby-trapped dialogue box, and then you can just plug the phone back in. Next time, don't touch that synch button. Just manually copy media using drag and drop. This problem does not always appear, so it probably resolves itself with a "transfer," assuming all the computers are registered under the same iTunes Store account. I didn't try, because most of my computers let me sync just fine. Personally, I hate privacy-invading DRM nannyware, so I insist on purchasing only DRM-free content.
(Sorry, kiddies, this tip won't help you pirate paid content, it just prevents iTunes from devouring the content you already paid for.)
Manually managing music on multiple computers with identical LPIDs requires you never to use the sync tabs on the iTunes page for your phone. If you try to enable any of the automatic sync tools, iTunes will warn you that it plans to eat your media. Don't do it. Hit the convenient cancel button and use drag & drop. That is the meaning of manual mode.
The very first time you enable manual mode, iTunes will still have to eat your phone, so be sure you have backups.
