Indiana Jones and the Raiders of the Lost Ark (as Cairo)

Jesus of Nazareth, Lawrence of Arabia, Soddom and Gomaorah, Gladiator (as Jerusalem)

In Angels and Demons as the Vatican

Used as Paris with Pulteney Bridge and Weir standing in for the banks of the Seine in Les Miserables

Onegin (as St Petersburg (Winter Palace))

used as the Louvre in the Three Musketeers (2011)

Gladiator (as Rome), Kingdom of Heaven + World War Z (as Jerusalem)

Passion of the Christ (as Jerusalem)

The Royal Naval College in Greenwich has been used in many films, but especially as Paris in Les Miserables (and the upcoming Napoleon) amongst many others.

Amadeus (as Vienna (Belvedere Palace))