I've been to at least 20 pho places in the South Bay, and two really stand out:

Pho Kim Long, on Capitol just south of the great mall near Milpitas, has it all. Their noodles are the best, the other ingredients are great, the bowls are huge even by Pho standards, the prices are low even by Pho standards, it's always packed by a mostly Asian crowd, and the name is really funny (find out the correct pronounciation of "Pho").

Near the SJC airport, there's a great place on 1st just south of 880 called Pho Bac So, which also has a bakery counter called Chez Croissant. You can check in for your flight, head over for lunch (or breakfast -- they open at 8), grab some pastries for the flight, and head back to the airport. Their broth is strongly flavored with warm spices; I've been told this is a more northern style. I've taken some Skywest pilots there and they eat there every time they're in town now.

There's a surprisingly good place in Reno, just south of Cal-Neva, called Pho 777.