Apple has replaced my 3GS twice.
This iOS 4 bug is pretty nefarious. If I were in an emergency situation, I could not make a 911 call for 90 minutes or so.
If I let my iphone 3GS battery die completely, then I have big problems.
If you are just skimming this post, I have done “Hard Resets”, and clean wipes on the phones.
I plan on installing iOS 4.1 immediately. I doubt I can make the phone much worse—but I may end up with a brick. If I let my iPhone 3GS run its battery down completely, it auto-shutdowns. Then, it takes ~1 hour to 90 minutes before I get the recharging chime (this time it took 132 minutes after 2 Hard Resets). Another 15 minutes later, I am presented with an unresponsive “Enter Password” screen. (It actually accepts the keypresses, but doesn’t act on it for another minute.) After 80 minutes, the phone finally unlocks, but the Apps are sluggish or just show a white screen. Letting the phone sit in that state for 10-30 minutes (like giving a recalcitrant kid a time-out), the phone FINALLY acts normally.
At this point, the battery indicator shows only a 5% charge after being on the charger for 90 minutes. I have tried both the iPhone charger and the iPad charger.
This “Charging Coma” bug ONLY OCCURS if I let the battery drain completely.
I have received TWO replacement phones and they both exhibit the identical bug. And yes, I did a fresh activation of both replacement phones (not from the iTunes backup file). The Apple Genius Bar guys ran diagnostics on each phone before replacing them. They all showed several unresponsive or crashing core Apps (such as Springboard and AOS-something or other).
The guys at the Apple Genius Bar finally admitted that others have been experiencing the same bug, and they hope iOS 4.1 will fix it. After that admission, they agreed with me that this was not a hardware failure, and giving me another replacement phone would be fruitless. They suggested that I don’t let the battery run down, and wait for iOS 4.1 to be released.
Most people probably don’t experience this bug, because they plug their phone in every night.
Doing a “Hard Reset” only extends (resets) the initial charging coma time.
If I simply leave the phone plugged in 90+ minutes to charge and sort things out without touching it, it works just fine, but require another 2 hours to fully charge.
So yes, I plan on installing 4.1 immediately and running the phone through the wringer. If I still experience the same bug, I’m not going to be very happy.
I see that iOS 4.1 has been released 30 minutes ago. Unfortunately, my 3GS is still in a charging coma after 2 hours. 
. . . An additional 20+ minutes later, my phone is now booted, unlocked and updating to 4.1 in iTunes. It is just now finishing downloading, and installing. BTW, the phone has been charging for 3 1/2 hours, and is just now up to 41% charged.
Phone is now fully booted up in iOS 4.1 and appears to be fine.
Well, I guess this post turned into a running commentary.
Hopefully, this does the trick :-/
Needless to say, I have just purchased another year of Apple Care.