The Van Heflin role in 3:10 to Yuma. Mostly because I find Heflin kind of annoying and I think Ford and Murphy would have played well off each other. Although the second half might turn into "is the farmer going to KILL the outlaw?" instead of "is the farmer going to yield to the outlaw's temptations?"
The Craig Stevens role in Buchanan Rides Alone. It's kind of a more sympathetic version of John Gant from No Name on the Bullet, and it would've allowed him to work with Budd Boetticher again.
The Charles Bronson role in Once Upon a Time in the West. It's the most bog-standard vengeful anti-hero role you can imagine, and just about any actor who could handle a horse, a gun, and a harmonica could have pulled it off. But it would've brought Murphy money and a way to stay busy at a time when he needed them, and it would have been fun seeing him framed in those endless closeup shots Sergio Leone liked so much.
I also think he would have been cool in 55 Days at Peking, but given Charlton Heston's horrific accounts of the filming, and the breakdowns Ava Gardner and the director suffered, I don't think I could wish that experience on someone who already had PTSD.