For me it's swimming. Running is too hard on my knees, and it's too easy to slack off using stationary equipment (plus, I feel like a hamster running on a wheel). It works every muscle in the body and will give you a nice muscular physique on it's own, something no other type of cardio can boast. I think it compliments weight lifting perfectly...swimming tones muscles, weight lifting builds muscle.
This is anecdotal, but every spring when I start my cutting phase I start off on stationary equipment (bike, stairclimber) because the pools aren't open yet. For the first 5 or 6 wks I get modest results, but nothing too dramatic. Then May rolls around, the pools open, and within 2 or 3 wks my body starts completely transforming. By early June, after 5 or 6 wks of swimming 5-6 times a wk, I am in pretty damn good shape, and will usually have lost about double the weight in the same time period swimming than I did using stationary equipment (during the winter I bulk, so I'll usually have about 15-20 lbs. to lose during spring).
But most importantly, I enjoy it...it's the only type of cardio I can say that about. Doing cardio sucks, plain and simple. I would say the best cardio is whatever kind you can actually tolerate doing on a regular basis. Forcing yourself to do something you hate just because it burns an extra 50 or 75 calories an hr. can be setting yourself up for failure, you're better off just picking something you like.