Hey guys (and girls),
I have been thinking and I've only come up with very few ideas, but still more than all the characters on the show!
Drones are kind of described as "the ultimate weapon", but that's not exactly true (especially since running out of ammo is a real possibility...make Anubis's fleet three times as large and the drone chair will be destroyed before the drones destroy the last ship and then those things will probably become inert and nothing is protecting Earth anymore (Anubis laughs about the bolted together piece of junk - pardon: The Prometheus - after all!)
I mean we don't know how fast drones are, but if ships actually moved (slugging matches like on the show kind of piss me off, in reality nobody would just sit there to let the enemy hit you, shields or not!) then dodging isn't a bad idea to start, then something like a CIWS (Phalanx, just a little more high-tech) might work, not to mention that shields (like the Asgard ones on human ships!) can take a fair amount of drones, but then again:
How about using a hyperspace-window to get rid of those pesky things? - "Drones approaching sir!", "Very good Lieutenant: Open up a hyperspace window close to the drones (or: in the middle of the drone-swarm, so that them dodging is impossible!)" - *Window opens and swallows most of the drones* - "Well done LT, now commence the attack!"
Well, just an idea (hell, you could even swallow the opening salvo of any fight...more if you give your ship several window-generators, so that you don't have to do it with the main one because you need that to move the ship!)