I'd be a little hesitant to call things like Krav Maga a martial art (but English is not my native language, so it's probably the (only) correct word for it). But I think the only things that can come close to Krav Maga in terms of effectiveness are other fighting methods focused entirely on reality, like those of other armies (I believe the Russians do something called Systema). In fact, I might even consider naming Krav Maga (or similar methods) 'cheating' in a comparison with martial arts like this, because there is virtually no style or philosophy behind it. The only criteria for something being included is that it is effective/practical. So if some martial art would have some technique that is somehow better than what is already in Krav Maga, and they'd know about it, it would simply be included.
Other martial arts are held back to the degree that they accomodate to adhering to certain rules or philosophies. The ones that will be most effective are the ones with the least rules.
Having said that, it also depends on the situation. If there are weapons involved for instance, or how bad you want to hurt your adversary. I'd say that in general a good (kick)boxer will probably beat a good judoka, but he has no choice but to severely hurt his opponent. A judoka might be able to neutralize in a less damaging way.