The problem with tweetdeck and twhirl and whatever else is that it turns twitter into IM, something constantly on that I have to check and that pops up alerts. I guess you could turn that stuff off, so that's what I'll experiment with.
I've turned off all alerts from Tweetdeck so it doesn't bother me when I'm focussing on work, and use 'clear' in each group when I've finished reading through it. Sometimes that means reading all the updates, others it's just a way of removing the old stuff I'm not going to bother with.
I only have two groups which basically split in to people I know well and want to read, and people who I don't know as well or are very noisy. The latter gets cleared a lot more without reading all the messages but lets me keep track of more local conversations and the interesting nuggets that come up occasionally.
The guy who makes Tweetdeck recently got some funding so he can work on it full time and hire in some extra talent, so it's likely to improve more rapidly than it has been.