I use Foursquare a lot. But you would not know it by looking at my Twitter feed. I rarely publish my checkins to Twitter... because frankly I can see how it would get very annoying after a while seeing everyone's Foursquare updates... especially if you don't use the service.
Up until now, there was literally no way to stop Foursquare updates from your friends from showing up in your timeline. Facebook has the "hide" option for the Foursquare application but nothing for Twitter. Tweetdeck changed this.
There's just one little hitch... this would only be on your computer. Currently the Tweetdeck mobile app (at least for iPhone) does not support this. I'm guessing in the future it might, but who knows. I haven't looked into that part yet.
Anyway, if you use Twitter on your computer a lot (Windows or Mac), head over to TweetDeck.com and download the client. Follow the setup steps and link your Twitter account (and whatever other account you want to add). The nice thing is that you do not need to have a Foursquare account to block the Foursquare feed.
Once you're setup and running... click the little wrench icon in the upper right to go to Settings. Click Global Filter at the bottom on the left. Now on the Filter Updates window, just type "foursquare" into the From Sources box (without the quotes anyway). This should filter all Foursquare updates from your timeline in TweetDeck. Pretty handy.
Also worth mentioning that if you add your existing Foursquare account to TweetDeck, it will ask if you want to do this automatically. But the above steps are helpful if you just don't want to see them and don't have an account.
There you go. No more Foursquare in your timeline.
3/11/11 UPDATE: There is now an app that will let you do a similar action on your phone (iPhone for now, Android soon?). Check out my How To post.
4/1/11 UPDATE: You can also do this on the twitter.com timeline using Greasemonkey and a script! Check out the How To.