Browsing this topic it seems some people only want to allow Indy's feat from "Crystal Skull". The things is even if we do it that way then Indy can tank anything and everything McClane can throw at him in a fist fight. Why well this...
http://www.youtube.com/watch?v=tnGuXXGgVq0
Their is absalutly nothing that McClane can hit Indy with that even approaches the desructive force/power/energy(what ever you want to call it) of being thrown up in the air by an atomic blast, and hurled at speeds faster then a speeding car while tumbling around inside a metal fridge, then dropping from a multiple story hight. Such as Indy was in this scene. In real life a person(hel any person in the fridge would have been turned into soup by that ride). In other words just using "Crystal Skull" McClane could hit Indy until his hands bled and still do no significant damage. This alone pretty much sums it up, but if we indulge the thread opener in his orginal intention to allow Indy all his features then We have multple examples of Indy's toughness. From sumberging with a sub in "Raiders" to taking a tank wrecking dive off a cliff in "Crusade"(and yes folks he must have ridden the tank over the edge, as the edge itself is visible and Indy is not on it), or the more mundane stuff like getting clubed, shot, burned, dragged behind vehicles, etc etc. As for fighting skill while both of them are generaly scrapers. Indy has showed knowledge of at the very least wrestling and boxing, as well as employing elbows, knees, feet, non-wrestling holds and throws. The truth is that Indy has actualy, to the best of my recolection shown far more versitility in combat then McClane. He also hits like a civ, we have seen him knock out two men with a single punch. His(Indy's) reaction time is also damn near in human. In "Raiders" a man is standing behind him, gun leveled on Indy pulling the trigger. Indy is able, grab his whip, uncoil it and hit the gun out of the mans hand before he shoots. Even if the assailent in question is slowish this is damn impressive for Indy. Some thing like 30 years later and a few years shy of 60, surrounded by armed Russian spec ops and after having spent at least hours crammed into the trunk of a car. Indy pulls of a similiar feat in "Crystal Skull". We also have the shoot out in Marions bar in "Raiders" where Jones switches back and forth between guns(.45 and .38) with out slowing his semi-automatic fire. We also have "Crusade" where Dr. Jones comfronted by Nazi soldiers(after having crashed threw a window and getting a vase to the head) was able to grab the SMG from one of them and shoot them both before they could respond. If the McClane supporter want to bring in luck, lets be honest they both have that in spades. The same thing can be said for sitational awarness and creative tactics. Both have taken out aircraft with cars and Indy fubaring a tank with a rock. Puts him equal if not better then McClane.
So to wrap up
Durability/toughness-Favors Indy. End of story. Nothing McClane has done even remotly compares to the fridge, cliff, or sub.
Strength-Its hard to call. Though Indy has pulled himself up by his toes while dangling upside down and he can definatly focus his strength better demonstrated by his single hit double KOs.
Agility/dexterity-Lets being honest Indy swings from whips runs across and threw booby trap rigged sites on a daily basis. He has this catagory in the bag.
Fighting ability-Again a a close one, but even look at the videos posted so far Indy has used. Knees, holds, throws etc. Even ignoring that he is demonstrable McClane equal if not better in just the bruiser catagory. Its also interesting to look at their records against martial artists. Every time McClane fights one he is in for the fight of his life-Asian girl in 4, general guy on the wing of the plane in 2, big German guy in 1. Yes he comes out on top(mostly due to luck and enviromentl factors), but he gets the snot kicked out of him in the process. Indy on the other hand fights off a crowd of them in the Club Obi-Wan in "Temple" and again against trained Thuggee fighters latter in the picture. Any body wanting to bring up the obviously trained boxer in the big German mechanic. Should remember that had she pressed her advantage at the onset of their fight the "ninja chick" in Die Hard 4 would likely have ended McClane. Remember he went down in moments and it was only after she had turned her attention back to her mission that he was able to get the upper hand. In other words the catagory goes to Indy as well.
Enviromental awarness, creativity, and luck. Are all about equal.
So in the end Indy edges, all be it barely in some cases, John out in nearly all areas and in the remaining they are about equal.
If some one wants to bring weapons in to the discussion remember while both have taken gun shot wounds. McClane has never taken a gun shot from a gun that has shown latter in the picture to go threw half a dozen odd guys, nor has he shown the marksmenship to make such a shot.
So in the end however you set up the match. Indy takes it.