Here are some fics set in Berlin and one in Prague...

daedalus, landing by Contra (M)

AU in which their city is Berlin instead of London. // Alternate Title: The Sky over Berlin

Maybe This Time by orphan_account (T)

There was a cabaret in a city called Berlin, in a country called Germany, in a Europe that just narrowly escaped the end of the world and was rapidly heading towards another attempt. And in that cabaret, an Angel and a Demon were dancing together. The trumpets signaling end times could have been playing, and they wouldn’t have even heard it over the music.

Angel on the Wall by Heretic1103 (T)

The Good Omens Berlin Wall fic you didn't know you wanted. So much pining coming from opposite sides of the Wall.

Mission: Ineffable by Andromeda4004 (M)

The Ineffable Mission Force is a top secret international network which will stop at nothing to make sure everything goes according to the Plan. Aziraphale Fell is a highly trained and trusted agent, deployed on a routine mission in Prague, until a betrayal results in him being branded a traitor and disavowed. Now, he must prove his innocence and track down the real double-agent with the help of an intriguing arms dealer, and a team assembled from other rejected agents. But who the hell can he trust when he’s playing both sides?

Puzzle Pieces by This_squirrel_is_nuts (M)

Berlin, May 10th, 1933 A big fire on the opera place is burning the books of at least 23 authors and one angel is making a desperate attempt at saving at least a few of them.

You're the Bad Guys by Nebz_AlphaCentauri (E)

Berlin, 1981. MI6 Agent Aziraphale has never been good at one night stands, but why not give ‘em another go in the middle of a mission in Cold War Germany? What could possibly go wrong? Agent Crowley goes along with the KGB as far as he can. But how far might he be willing to go for a certain British secret agent with blond curls and a penchant for waistcoats?