iOS 5 OTA sync went over 3G instead of wifi
Did the iCloud sync over 3G last night? (My iPhone and Mac were both on my home wifi network that did not break during the night)


No. iTunes can only sync over Wi-Fi. Any automated backup to iCloud can only be done via Wi-Fi as well. However you can initiate a backup via 3G but not a sync since iTunes can't "see" the device if it's not on the same network, and in most cases you will receive a warning that it will use your data plan.


  I was playing with the iMessage feature and I sent an email to one of my other (non-AppleID) email IDs from it, just to check. The email came thru with the email ID being my_phone_number@mms.att.net and this was when I got that 90% email from AT&amp;T.


Highly unlikely. Messages sent via iMessage, unless they contain huge images, are even smaller then most emails. The system also sends it as one single message and is not considered email actually.


  What caused my 3G plan to be over used? The MMS or iCloud?


If you manually started a sync with iCloud then that would be the case, however, your iPhone will always use the Wi-Fi first, and it is something I specifically tested during beta, if the iPhone can't find a Wi-Fi connection to automatically sync or backup it won't initiate the processes at all.

If you sent a massive message with images via iMessage, probably, but iMessage is not considered email, and it is sent via the Apple servers. 

I would suggest you look at other areas of your phone, or most probably and app that is abusing your bandwidth. One thing it could possibly be is automatic iTunes Store downloads where you have an option to turn on Mobile Data for downloads. You can find this under Settings -> Store.