So it looks like Twitter is going to be handling this using "Lists" .
TWEET: RT @andybeal Be Warned, Twitter Lists Will End in Tears!http://bit.ly/edRfS
and see Twitters blog entry here:
http://blog.twitter.com/2009/09/soon-to-launch-lists.html
Sounds initially like a good plan.  I think that it will be essential for twitter to help users organize the people they follow at the core so that they can handle the amount of tweets they are seeing in their stream.
Facebook already has their own list functionality: http://www.facebook.com/help.php?page=768
I wonder though if these lists will sync somehow with the groups in tweetdeck and other twitter applications.
I am hoping that all the applications will implement the API as soon as its available. I am mainly speaking of applications like tweetdeck, ubertwitter, socialscope, digsby, peoplebrowsr.com, and the many other tweeting tools that are out there.
It will also be interesting to see how things play out with TweepML. http://tweepml.org/

TWEET: RT @TechCrunch: Twitter Lists Competitors Respond: We Can All Get Along http://bit.ly/1Tq9d9 by @parislemon
TWEET: 10 Issues with Twitter Lists that TweepML Addresses Today http://bit.ly/yWBkc
 
The ultimate hope is that these twitter lists will also someday play fair with my Facebook lists.
Maybe after all that is why Twitter called their upcoming feature "lists" and not "groups".
In the end they are all just "channels".