A recent Wired article discusses the impact of biometric passports on the operations of intelligence agencies. The problem is that with such passports, it is much harder for a spy to assume a new identity (as the identity is linked to a biometric property). Moreover, hotels typically scan the passport of all guests checking in. This data can be cross-checked in real-time with data gathered at the border crossing and entered in immigration databases to see whether a guest officially entered the country, or whether his passport data appears to have changed in the meantime.
The following quotes make very clear that intelligence agencies will stop at nothing to prevent detection of this (and by extension, for anything else).
"Just before I left, they were gearing up to make a request for CIA officers to recruit foreigners with access to immigration databases," said the retired NOC. "I'm sure that several people made careers out of just this kind of operation, much as some officers did when the NSA suddenly lost millions of access points to intelligence when the world switched from microwave towers to fiber optic lines --- whole departments were formed to recruit telephone company assets in foreign countries."
Israeli's passports are useless for their own Mossad agents: Israeli's are typically denied access to the countries their spies are most interested in. So they have to create fake foreign passports, claiming to come from the EU for instance. Another quote from the same wired article.
Mossad puts its documents through test runs, said Ross, who retired in 2001.
"We get into, say, France, with a document, then change our appearance, then go into Germany and see if they pick up the physical change, to see if the two speak to each other and say, `Wait a minute, is this the same guy? Before he had a beard and glasses, and now he's clean-shaven and wears contacts.'"