There have been like a million 47s...
Marshall wanted to get 47 shots in the lipstick camera in the first episode
Marshall was held by Suit & Glasses on the 47th floor
The magnatometor that Sloane stole from that bank last year was in box 4747
There was of course page 47 of the Rambaldi book, which contained the Prophecy
Syd was held by the Covenant in Room 47
The server on the plane that belonged to the Alliance was Server 47
There have been soooooooooooooooo many more, especially in Season 2, these are just off the top of my head.
I honestly don't think we'll ever know the significance, just that it's a prime number and probably JJ Abram's favorite/lucky number.