According to this page, the 5-windows were the most common version. However, it was not the "coolest" looking, so it was most likely it was the least preserved (and as said below, the least-reproduced). This is pure Wayne speculation.

I don't know all the models below to know which as 3 or 5 window, and I didn't look them all up, but you can quickly see 5 window was the most common manufactured. Number manufactured data from: http://www.roadsters.com/deuce/

Cabriolet____________________6,091
Convertible sedan______________926
Five-window Standard coupe__51,794 (5-window)
Fordor sedan_______________37,363
Panel delivery________________6,122
Phaeton_____________________2,490
Roadster____________________12,597
Sedan delivery_________________400
Station wagon________________1,383
Sport coupe_________________2,911
Three-window Deluxe coupe___22,148
Tudor sedan________________124,101 (5-window)
Victoria______________________8,580

Edit: Man, my spelling stinks + good thought from below.