If you have never been to SD before, Guacara Taina, is a must. Really cool place deep down in a huge cave.
Also:
Jet Set, kind of far from downtown but still cool
Jubilee, next to Jaragua
As previously mentioned Kokomos on Tiradentes, but it is not really a disco, just a cool place to have a few drinks on your way out.
Disco de noche on the Malecon is open very late, maybe 7:00 am, but many patrons appear to be on drugs in the wee hours.
If you want a small local place with no tourists, try Kassandra on avenida venezuela.
Cafe Atlantico
enjoy!