None of these are indie games.

That's a bit fuzzy. Half-Life had a budget of around $1M back in 1998 under its original publisher Sierra On-Line. It had to be saved by Gabe Newell, who went out of pocket to keep it afloat.

This, compared to peer AAA titles like FF7 ($145M), Shenmu ($47M), and Wing Commander 4 ($12M) made it significantly underweight. Even Game Freak's break out title "Pokemon" is estimated to cost north of $10M. As Sierra On-line was a historically famous publisher on the brink of bankruptcy, it's debatable whether their dying gasp constitutes a "legit" indie title or not.

But whatever you can say about the original, the sandbox of second-tier mod games that it spawned - Counterstrike, Team Fortress, Day of Defeat, Natural Selection - certainly qualify.