I started researching pumps about six months ago and was amazed at the variety of mechanisms available. Check out http://animatedsoftware.com/pumpglos/pumpglos.htm for a bunch of cool animated pump illustrations (the ones with asterisks are animated). Pumps are some of the most common machines on Earth yet little understood. Below is one of the more interesting rotary pumps. It would be very difficult to build but it illustrates the wide range of possibilities available. You might also find some of the diaphram pumps interesting.

For me, the appeal of the piston design is availability of off-the-shelf parts, ease of construction and profile; by profile I mean that it doesn't stick out of the bulkhead or deck in a way that could entrap the paddler or interfere with a reentry. The drawback is in the piston which requires a very good seal in order to avoid blow-by. Otherwize I would say the sky's the limit.

: It seems to me that everyone is wedded to the idea of cylindrical pumps.
: Isn't there a way to put a rotary type pump with a hand crank through the
: deck and/or hull in front of the paddler? ...
: And doesn't anyone make a bellows type pump? Hold it between your hands like
: an accordion and pump away. I'd think that one of these equipped with big
: hoses and valves could empty a flooded cockpit faster than with any
: cylinder pump with less effort.