Netserk, in the 2009 Giro, Sastre did finish fourth on the road, but he was moved up to third after DiLuca was stripped of his second place finish. Menchov, of course, has practically made a career of moving up on the podium as guys ahead of him got busted.
Found another: Tony Rominger. I didn’t realize he came so close to winning all three GTs. Three Vuelta firsts, one Giro first, one TDF second.
Here are some great riders who didn’t podium in all three GTs (in many cases, because they never or rarely entered one of them):
Gino Bartali
Fausto Coppi
Louison Bobet
Bernard Thevenet
Joop Zoetemelk
Greg Lemond
I think riders who podium in all three GTs, if they don't win them all, tend to be second tier. The greatest riders tend to focus on the TDF, of course, and maybe one other GT.