Free-standing water coolers have always been the traditional choice and probably remain the ideal solution if you have sufficient space. Being that little bit bigger they tend to become a focal point and therefore engender the age old "water cooler chat".
Desktop versions were devised in response to those with smaller space. They are ideal for the home (e.g. sitting on a kitchen work surface) or any other situation where space is limited. They tend to be a little cheaper but on the downside the water cooling capacity (litres per hour) is usually smaller. If you go with a desktop bottled cooler (as oppossed to a plumbed-in cooler) then the bottles will be smaller, meaning you have to change them more frequently.