Academgorodok is a real city in southwestern Siberia, dedicated to science...
When the computer starts suggesting Alpha sectors etc... I start making up my own names. If nothing comes to mind, I start taking them from song titles from random records in my cd-shelf... I found the songs by In Flames' (a swedish death metal band...) first albums to work fine; Behind Space, Lunar Strain, Starforsaken, etc...
And of course, names inspired by real place names, or myths etc.. like Jotunheim, Kalevala...
When renaming conquered cities, I like to somehow "corrupt" the earlier names; New Jerusalem -> New Babylon, Morgan Industries -> (my name) Sindustries, University Base -> Punyversity... etc. Whatever comes to my mind.