We were making commercial games from our bedroom in the 80's and 90's but we were not calling ourselves "indies".

I'm pretty sure industry comparisons with indie filmmakers and indie music bands started before Braid (IndieCade was founded in 2005), but as a widely used and popular term, I think it's fair to choose 2008 as a turning point [1], and Braid as the poster child.

[1] http://www.gamasutra.com/view/feature/132041/the_state_of_in...

That segment of the market has gone through many names. I remember playing Wolfenstein 3D and Doom as "shareware" which defined a fairly large chunk of the indie market back in the early 90's. Before that there were people putting games out on BBS systems that you could buy the full versions of by mailing in checks of money with your return address. You don't get much more "indie" than that (but you can).

The difference would be that at the time, there weren't a lot of / big publishers to be independent from.