Is it better for me to fridgerate all my bottles after 3 weeks of conditioning or should I just keep them at room temp and only fridgerate the bottles when I'm ready to drink them? I've heard a little bit of both sides but was just curious.
Chill a couple for a good day (or more) first and check carbonation. Then refrigerate as much as you want because you'll want them to be able to chill for well over a day anyway. If you have the space then why not? There's no technical reason to keep some at room temp or not unless we're talking about a beer that should be conditioning. In that case, you'd basically want to keep all at room temp for weeks and weeks...and months.
I don't fridge at all, I like my homebrew not that cold, about 6%, malty, hoppy! and about 12-15C that's a bit less than normal room temp.
I suppose that's what you guys would expect as I am in the UK.