Well, I've now upgraded two machines to iTunes 9.0 and two iPhones to 3.1. Both times I upgraded iTunes before the iPhone.
The first one, attached to a 17" MacBook Pro running Snow Leopard is an original iPhone (not 3G) which I use as a bedside clock/alarm/streaming radio device using WiFi as it no longer has a SIM card in. This is the first time that the upgrade process has not asked me to put a SIM card in and re-activate it. Looks like they now realise that the units are indeed "the best iPod ever made" rather than a phone with an iPod! The only issue I suffered was that it forgot the name of the iPhone (was called "iPhone Original") and now just calls it "iPhone" - not a big deal.
The second one, a 3G is attached to a Windows XP machine and this one had no issues at all upgrading iTunes and then the iPhone software.
I have over 1500 Apps listed in iTunes and I can tell you that iTunes 9 now starts faster, uses *far* less memory (we're talking about half a gig previously - now under half that) and scrolls through applications *much* faster.
Other than the first backup since the upgrade, every other backup has been back to a fast speed again.
A happy customer. 🙂