I was searching for some information on the show to do with a QR code that is on one of the cell doors in New Alcatraz and came across this article A Box Of Mysterious ALCATRAZ Stuff Shows Up At Badass HQ.
Update - there is some more info and pictures of the items in the box at MovieWeb.com
It describes some marketing material sent out to bloggers and mentions that a review of the Doc Soto Alcatraz book has some letters circled which form the words "Legends Of Alcatraz".
So if you go to the website http://legendsofalcatraz.com then you get presented with a puzzle. (If you go to http://legendsofalcatraz.com you get a Fox TV branded version but if you go directly to http://legendsofalcatraz.com/home you get the standalone site.)
The solution to the puzzle is below, click to reveal it.
When you enter the answer you get this information (Click to reveal)
There is also a link to the @LegendsofAlcatraz twitter account which shows this tweet.
Finally the numbers on the answer page seem to be co-ordinates and indeed if you enter them into any online mapping site they take you to a point in the middle of Alcatraz (of course :-) )
The menu card has some missing letters - C M X I V - which appear to be Roman numerals and translate to 914.
Entering 914 in the answer box shows you the next part of the puzzle.