The issues I hate the most when building a new system have to do with size compatibility. The biggest culprits of these issue are tall memory heatsinks and CPU coolers. Thermaltake, one of the leading brands in CPU coolers, has a new series of CPU coolers that promises to eliminate both of these with their new series, the Thermaltake NiC.
The NiC, or Non-interference Cooler, is designed to work with any memory kit on any standard sized motherboards without compromise. The NiC series includes the F3, F4, C4, and C5 which have 160w, 180w, 200w, and 230w TDP rating. The largest of the NiC series, the C5, has five 6mm heatpipes but does not interfere with RAM at all.
If you are in need of a sizable CPU cooler, but refuse to limit your RAM selection, then the NiC C5 is the cooler you are looking to buy. If you are building a system with a smaller board and/or a CPU that generates less heat, then you still have options.