Are there any tabletop apps to allow you to play warhammer 40k with friends in other cities?
As @Skeith mentioned, Games Workshop LLC is very vicious when it comes to protecting their Intellectual Property license, so it will be very hard to find anything designed for this on purpose.

That being said, Steam recently released a game called Tabletop Simulator, which, with a lot of work, could probably be used as a tool for this (right up until GW catches on and their lawyers destroy the life of whoever is supporting the mod).