Gamasutra's been rounding up the top titles of the year in a variety of categories; up recently were the top five 'indie' games (plus ten honorable mentions).
People have been having hissy fits because because some of the downloadable titles of the year (e.g., Braid) weren't on the list, but take note:
The games picked are the editors' choice, and span PC free-to-play titles released during 2008's calendar year to date, with a mixture of Flash and Windows executable games. (Many other fine pay-to-download games for console and PC that might be considered 'indie' were ranked in the Top 5 Downloadable Games earlier this week.)
There are some nice titles on there if you haven't been keeping up with the free indie game scene; the other lists are worth a looksee too. I always like seeing the yearend roundups, even if I don't agree with all of their picks.
Gamasutra's Best Of 2008: Top 5 Indie Games [Gamasutra]