Thrifting in Berlin
Berlin has a lot of Second Hand stores, but the big ones like Humana and Colours are often overpriced, because "Vintage" clothing and items are so much more popular in Berlin as in other cities in Germany.
My ultimate insider tip for inexpensive second hand shopping is the flea market at the community center in Karow. This is actually the location where we got married in 2014 and they have a flea market every two weeks from April to November.
Thrifting in Munich
Weißer Rabe Gebrauchtwarenhäuser - White Raven Second Hand Goods
There are two branches of the Weißer Rabe thrift stores. I like them a lot, because they got everything from electronics, houseware items, furniture, books to very inexpensive clothing. They remind me of the Goodwill stores in the US, but on a smaller scale. They employ people in "difficult situations" as stated on their website and fund various charities with their earnings.
Landsberger Straße 146
Kaufhaus Diakonia Secondhand They are very similar to the Weißer Rabe thrift stores. It's a little out of my way so I don't visit them as often, but they are worth checking out for cheap furniture and books. Also children's audio tapes, if you're into that (I am).
Kaufhaus Diakonia Secondhand
Dachauer Straße 192
80992 München - Diakonia Second Hand Department Store
AWM Halle 2 - Garbage collection Hall 2
It's right by the Isar, so stop by and be amazed.
Abfallwirtschaftsbetrieb München - Halle 2Sachsenstraße 29
They also have a useful guide to second hand stores.