I was reluctant to install the patch now that I had my iPhone "where i wanted it" with apps, mods, new icons, etc. But I thought, what the hell...so I did the following
1. Sync with iTunes to get a good backup
2. Restore the phone via iTunes which brought it up to 1.0.2
3. Re-Activated and re-synced my settings.
4. A quick jailbreak with ifuntastic, reload SSH/SFTP
5. Throw back on my ringtones, carrier logos
6. Install the Installer.app, sit on couch and re-load my apps.
Total time, 20 Minutes, didn't swear once, wife didn't even notice.
If you take the time and do it right, it's not an issue, even with a highly modded (albeit activated traditionally via ATT) iPhone.
Is it a pain? Sure. But I like my apps, the couple ringtones I added, and being on the cutting edge. I guess it's the price we pay.
So go for it, do it slow, and right, and you shouldn't have any problems.
Just curious honestly which apps you use that make it worth going through even 5 mins of extra trouble? I couldn't care less about custom ringtones but am curious as to which 3rd party apps you regularly use on the iPhone. If I ever did it I feel like I'd get tired of the apps pretty quickly but then have the added headache of a complicated update path.
Don't see any apps that are compelling enough for me right now.