A 99 was a frozen dessert that was superior in value to a choc-ice.

When a Cyberman snuck up on the Tenth Doctor and said, "You will be upgraded", the Doctor — lost in thought about the virtues of choc-ices — initially believed that he was eligible for a 99 at the same price as a choc-ice. (COMIC: The Power of the Cybermen)

The Eighth Doctor joked that chocophobics would be the only ones to order Mr. Whippys without flakes. (AUDIO: Memory Lane)

During a visit to 1925 Milan for an ice cream, Rose Tyler said that if they didn't do 99s, "that's Italy's loss!" (COMIC: The Futurists)

Behind the scenes[]

The Power of the Cybermen never uses the term "99 Flake", but such is what "a 99" means in modern British vernacular. Contextually, too, it makes sense that the Doctor means a 99 Flake, since a 99 Flake would indeed be an "upgrade" from a choc-ice.