Swype? I've heard many iPhone owners wish they could have such a utility on their phone.
WinAmp WiFi sync? Wasn't this similar to an app Apple rejected and later popped up on Cydia? I know I've heard a lot of interest when it was submitted to the AppStore.
Barcode scanner? I know, I know. Both can do this today, BUT the G1 was capable of barcode scanning as a result of autofocus and preceded the iPhone's ability.
Chrome to Phone. Probably classifies as a system enhancement. Same goes for the ability to wipe and restore all over the cloud. Since Gruber disqualified it as part of his article, it doesn't get mentioned but this is huge, IMO.
Grooveshark?
I'm not taking sides as I own both and appreciate the similarities and differences in both platforms.