Shoes are a very personal choice, me...
For general use = Keens
KEEN Footwear - Mobile
For more dressed look = Rockports or Sperry
These are particularly comfortable Barefoot Boat 2 Eye | Men's Boat Shoes | Rockport
For poor/cold weather = HH Deck Boot HELLY WELLY - Men - Inshore Racing | Helly Hansen Official Online Store
I don't think flip flops are safe on a boat, nor do I like bare feet, too many things for me to F up my toes on, and I like working toes = balance.