Long rods reduce peak piston acceleration, and reduce the angularity of the rod relative to the crank (meaning that the piston is marginally more efficent at pushing on the crank). They also hold the piston near TDC for longer, meaning that the rate of increase in compression pressure is more gradual, and that ignition timing is less critical.
This is all good stuff.
In theory, a long rod can make the engine more likely to detonate, as the additional time the piston spends at/near TDC can prevent the combustion gases expanding as fast as they want (poor explaination, but hopefully it makes sense). In reality, it is very difficult to find anyone who even claims to have experienced this phenonema - if it exists at all, it has far more to do with large bore sizes (4"+) requiring lots of time for the flame front to travel across the combustion chamber.
Long rods also increase the height of an engine, which is rarely desirable but not often a problem.
The trend in the last thirty-odd years for rod:stroke ratio, has been clearly toward longer rods in all sorts of engines.
Four strokes have also had a clear trend toward shorter pistons - the reduced side loading of longer rods has allowed this.