The Rolls-Royce Merlin gets my vote as the best military engine of the last 100 years and the RB211 for the best Civil engine
while I agree the Merlin was hands down simply the best Military engine of its time, the RB211 hardly deserves the distinction of the best civil engine - it has failed a number of times in high profile incidents with BA and other airlines - I've noticed a higher failure rate when compared to GE and PW. I would vouch for the JT8D engine which was adapted for so many different aircraft and uses, and is very reliable.