Cowl flaps, are doors that regulates the cooling of the engine (not used on modern jets)
When more cooling air is needed you'll open the cowl flaps
Winglets are - like Craig said - drag reducing, thus also fuel saving.
But the winglets also increase the overall spread of the trailing egde vortices, creating more lift at the wingtips.
Quoted from Boeing Aero Magazine
"* Creates more efficient flight characteristics in cruise and during take off and landing
* Approx 4% increase in range (130nm for the 737-800)but you must be at LRC or OPT altitude"
LRC stands for Long Range Cruise and is available in the FMC's CRZ page.
As you can see, winglets are no use for short flights.