wp-content/plugins/.It's proven quite useful in preventing automated comment spam from even reaching the moderation queue, let alone appearing on the site. It is technically a CAPTCHA, so its presence does mean that any commenter who isn't logged in (and if you don't offer registration, then none of your commenters can be logged in) has to jump through one more hoop in order to comment. On the other hand, it's completely accessible, unlike image-based CAPTCHA, and you can have a lot of fun with it if you're creative with your challenges. Some fun and interesting challenges people have used:
The most obvious way is that a challenge will appear in your comment forms. The other obvious way is that you'll suddenly stop getting reams of comment spam.
The plugin adds a function called gatekeeper_pose_challenge() which you can use to control where in the comment form the challenge appears. To use it, you edit your comment form by adding the function call wherever you want the challenge to show up. You can either pass the markup to be returned as a parameter of gatekeeper_pose_challenge(), or you can alter it using the "Markup template" section of the Gatekeeper management page.
Because there is nothing to prevent an enterprising soul from porting Gatekeeper over to, say, Moveable Type. In such a case, I'd expect them to call it MT-Gatekeeper.