[from a comment posted elsewhere]
There’s a goth club listing at http://etoile.de/; Berlin is in the section ‘PLZ-Bereich 1′. You can probably read through the genre descriptions and club addresses without needing much German.
The Kit Kat Club is — well, if you’ve had it recommended, you probably have an idea. I like it, although I’ve not been since a couple of years ago, when it was in a different venue. [I stopped going after seeing a page on their site seemingly saying that they don’t want Turks or feminists in the club. Probably it’s just an unfortunately-worded page, but it didn’t make me want to go back]
Also on the sex end of the spectrum, check out Insomnia. It’s a fetish club, with a monthly goth night called ‘angel in bondage’.
K17 is the largest and most regular goth club, with a big dose of metal and industrial. On a Friday or Saturday, they generally have four floors: one trad goth and 80s, one electro/industrial, and two small ones for metal. The venue is ugly as hell, but also huge.
If you fancy going out on a Monday night, Duncker is a lovely smallish club, with a lot of regulars and a friendly atmosphere. They (always?) have some kind of barbeque-type food in their back courtyard, and will keep going until Tuesday morning. I think there’s also a small goth market there every other sunday afternoon (http://www.darkmarket.de/).
Other places: Kato is more rock-oriented, and has lots of smallish live gigs. ACUD and Sama-Cafe are squats (perhaps legalised; I’m not sure), which do goth/wave nights. They’re incredibly cheap (to make them accessible to everybody; do pay a bit more if you can!). Expect plenty of shabby-looking punks and people out of their heads on (cheap) Sternberg beer.