I use one of a few custom lists of real place names I'm familiar with: towns in Scotland; towns in the UK; towns in Germany, and towns in Japan. That way I'm never confused about which planet is which when there's a notification. I know that I have an Adv. Fac and core fab on Thurso, I know that Inverness is next to my homeworld and I can't help sniggering that one of the AI homeworlds is in Auchtermuchty. The familiarity of the names allows little ambiguity as to where things are in my mental map.
Granted, it may seem a little less sci-fi, but lots of names for "new" places are just copied from old places anyway, so why wouldn't people name planets after towns or cities from earth? An obvious example is that Dallas is a small village with a population of under 200 people. All the Dallases in America are named after that one.