There are many different opinions - if you search, you can probably find some threads on them. I would say it boils down to, if someone says it to you, take it as written and don't apply any hidden agendas or tone to it. They're probably not meaning any harm. On the flip side, you are free to use it how you think is fair - if you think you should only say it when you lose, then go that way. But don't assume that others going a different way (from saying it when they win all the way to not saying it at all) means they are being rude, sore losers, poor etiquette, etc. Short of someone directly insulting you, or harassing you (eg. play faster, etc.), most people are probably not intending to be offensive to other players.
I personally only say good game when I think it was a good game, typically a hard-fought/close/well-played game. I feel like saying it on every game devalues it. But that is only my opinion and I accept that others see it differently. Sometimes if others say it first I will respond, but as I mostly play turn-based, I only do that if it's within about 1 hour of game end, as I personally find getting a response about a game that ended hours ago is quite annoying. But again, that's just my opinion. I may feel annoyed, but I don't say anything to another player who happens to do that.