It's a toss-up between Raiders and Temple. Sorry Crusade, but that movie was too comical for its own good -- Half the beating Indy took didn't feel like it hurt him much, or we didn't wince or feel it as an audience. With Raiders and Temple though, being heavier-duty films, when Indy got hurt, we got hurt with him. Crusade had me laughing. But Raiders and Temple had me exhausted. Still, I put my vote down for Raiders. The desert chase sequence, to me, is the ultimate example of Indy's character:
He is determined to get that artifact, no longer because he's after it himself, but it's personal, and he'll be damned if he lets the bad guys keep it, and so he'll endure the worst of beatings and keep going.
Favorite clip: When Indy slams the truck door and resumes the chase with the Raiders March raising in volume. The look of determination on Indy's face says it all. It's on par with the best moments of Rocky or when Luke listened to Obi-Wan in the Death Star trench and focused. All the beating the hero takes, all the pain and doubt, in that moment, you feel it, you believe it, and you feel as he does -- Gonna win! No matter what.
So, for me, judging Indy's worst beating isn't how dusty he is, how shredded his clothes are or how much he's screamed (although those are all good measurements -- kudos to those who brought them up), but the measure of Indy's beating is based on the moment of his focus, of just how badly (or madly) he wants to beat the bad guys.
On that note, a runner-up: In Temple, right after he says "All of us . . ." and the Thuggie guard looks up to just see Indy standing there with a look of death on his face -- THAT'S how you know the pain a hero has been through, of just how pissed he is when Act III begins.