General container question

Sorry if this is a duplicate - I had a PEBKAC moment...

Hi folks,

I'm not sure who caught sight of the article that was posted to slashdot 
a few days ago about that Handbrake project dropping DiVX/Xvid and/or 
the AVI container format altogether.  There were a lot of comments about 
how AVI is an obsolete container format and has all sorts of issues with 
audio and visual sync, how it causes programmers endless headaches, how 
it doesn't support chapters and subtitles, etc.  As far as transcode 
users are concerned, what are the preferred container formats for 
generic audio/video content these days then?  OGM?  MKV?  I have up to 
this point been transcoding my mpeg2ts to xvid in an avi container... 
perhaps I should use something a little more modern?

Thanks for the input folks.

-Mishehu