With all the recent problems, should I buy 27'' 3.06 iMac or hold off?
Also, what are advantages of buying outside the Apple store (I can get the Edu discount from Apple)?
I would buy now. AFAIK, most of the problems are now solved and when you come to places like MacRumors, you'll always see people having problems as they come here and ask for help.
There is no guarantee that an update would be trouble-free