No real preference for any of these modes in absolute. IMHO, the layout of typical high-end systems is too simple to create a real advantage for the intrinsic noise rejecting capabilities of true balanced equipment connected using balanced cables. Then we are just listening to implementations of a particular topology.
If a balanced system is implemented with transformers you get the sonic signature of the transformers. I have some experience with them - the best I have tried is the great SMC Audio Flex-Connect
http://smcaudio.com/products/flex-connect/, that operates miracles in many systems. However as its gain (attenuation) is -12dB I am not sure of the real cause of the improvements - too many factors were being changed when I inserted it.
Usually balanced systems are much more complex in terms of electronics than unbalanced systems - but not all of them. An integrally balanced system from input to the speaker output does not suffer from the typical pattern of distortions created by the inverting/summing input stage of most equipment that can accept both type of signals. But such systems are the exception.
The great drawback of the balanced/unbalanced is that we should have duplicates of cables to compare equipment in equal conditions - most of my better cables are balanced, I currently feel that sometimes I am not giving a fair opportunity to single ended equipment in my system, unless I use the Flex-Connect, that strongly distorts the results of the comparison.