The newest version of the Market (3.1.6) allows you to rate apps now. I'm not sure exactly when it was released, but it was rolled out to the Motorola Xoom as part of the 4G LTE upgrade. There's an XDA thread for the new version which has discussion about installing it on other devices (I got the update when my Xoom was upgraded, so I'm not sure about stability and the like). I'm not positive if it requires a specific version of Android to work (i.e. 3.2) or if it will work on all versions of Honeycomb.
Rating works pretty much like the phone version. You go to the app's page on the Market and there is a "Rate & Review" link on the left side of the page.