I prefer to be barefoot, weather permitting and despite being a bit of a klutz, as a general philosophy, to show off my toenail polish, and because I think bare feet are "grippier" and give one more warning when a slip is imminent--that extra second to grab something or plant my feet may save my noggin.
Otherwise, here are the shoes I'm often wearing:
Sanuk flip-flops (couple years old, very grungy, and oh-so-comfortable, love, love, love these) (I think the "shoe" style ones would also be great, I just need to get a smaller size so I don't walk out of them).
Sebago Docksides (circa 1998 that are beginning to separate from the sole, but served me well many years in good and foul weather boating in Miami).
Dankso clogs (haven't had any problem running up the side decks in the rain to adjust lines in them, or running down a wet finger pier, and they simply will not slip even on a grease-covered kitchen floor, but they do change your center of gravity and not for folks with rolly ankles).
Reef flip-flops (haven't really been tested in wet conditions yet).
Uggs (only when no snow or ice possible or too slippery).
North Face snow boots (if snow, ice, or rain).
LL Bean Wellies (awesome for rainy days and for sitting in the dink when she needs bailing out).
Croc ballet flats (haven't had any problem so far; useful as my change of shoes so I can get back down the pier drunk after a night out in spiky heels that would get stuck in the dock).
I have some Teva-style shoes from Merrill I haven't really tested aboard (they were for summer afternoon thunderstorms in Miami when I needed to wade back to my car). My ex called them "graduate-student shoes."
I like my Birkenstocks, but as I've had tides requiring me to sit on the pier and jump down to the boat, I worry about them falling off and into the drink.
I had some decent Sperry's a long time ago, but were never particularly comfortable and all the ones I see now have weird bling on them.
I worked on a fishing charter, and almost reeled in a sizable Rockfish, wearing high-heel wedge espadrilles that had a wonderful flat sticky sole. I probably had better balance than just about anyone on the boat; definitely than any of the passengers. I'm on a boat because I don't believe in following anyone's rules, and that includes whatever the yachties et alia say I should be wearing.