The ability to sign into an Identica account as well as a twitter account to see your timelines from both services in 'the fall'.

Desktop application to run on the users system (OS X, Windows, linux) so they can see updates in real time with out having to use a web browser.

pause and speed shortcuts would be cool

Sometimes the slowest speed "Default" ist too fast. Why did you remove slower options from earlier versions?

I would like the option to pause the feeds when you click a link so that you can catch up to where you left off when you finished viewing the link

prevent tweets that you've already read (generated by search) be displayed when u reload browser

And especially the keywords ofcourse :)

Would be nice to ignore all the tweets generated by your chosen search terms that you've already seen. A selectable time bracket (6, 12, 24, 48, 72 hrs) would be useful.

When hovering on a username, various stats are displayed. It would be great if that could include whether that user is following you back.

Text to speech would be great for the visually impaired. It can be done via RSS - or maybe check out this Firefox plugin/API

Already tweeted this, but just adding here:
The URL expansion happens on any mouseover, so even when I'm going to click on something else they get expanded, which is a bit annoying.

Add a tiny delay maybe?

some of my search terms are found from one company that makes many twitter users and sends out the same posts to each of them, so it appears I get a lot of dupes in the list. I'd like to block the entire fake user in one click.

As People are more likely to put country than location, I think it would be helpful to have a country-list in drop-down. Within that, you could filter multiple locations, i.e. England / Britain / UK or clear up duplicate place names like London, British Columbia

I want to use TwitterFall for church, but don't like having to enter all the bad words in the exclusions panel every time I log in. Any way to remember them?

There is a coloured button next to Tweets, Mentions and DMs but none of these open the colour picker

I like to set up a large monitor with a stream to show the backchannel at events. This monitor would be unattended and so the "display on hover" functionality doesn't help. An option to display linked images inline in the stream would be great.

I think somewhere by the custom search you should include a link to the twitter search operators, and (maybe), the twitter advanced search page - you could also provide a text field which can 'eat' the url creater by the twitter advanced search and create a custom search (though the workflow for that might be beyond Joe User).