Joe's in Windhoek for the ambiance and beer, the food is OK.
Best German cuisine in Namibia is at Brauhaus in Swakop + it's a treat seeing the waiters in action. How they take and remember orders for tables of 12 without writing anything down is beyond me. I cannot even remember what I had for breakfast.
Whilst we're in Swakop make sure to go past Village cafe for breakfast, that place has awesome food and an even better vibe! To echo Man from Nam - try the Terminator 1 or Terminator 2, just don't plan anything for the rest of the morning

Lastly, I cannot resist the jaffels and filter coffee at Eagles service station in Henties:-)
If you're in Damaraland pop by Brandberg Rest Camp in Uis for a Hungarob burger and a cold draught.