What features from Lion will be lost when upgrading to Mountain Lion?

Of course. In adding features, the behavior of previous features changes, not always for the better.

If you find features that were present in Lion but missing in Mountain Lion, please edit this answer to add your contributions to this list.

• Mountain Lion drops support for some models of Macs supported by Lion.

• Clicking the top right corner no longer triggers Spotlight (Spotlight's menubar icon is still present, adjacent to the new Notification Center icon).

• The battery indicator in the menubar will no longer offer to show the remaining time.

• X11.app is included, but that app alone no longer provides X11 functionality. When the user first runs X11.app – or an app that requires X11 – a dialogue guides the user to Apple's article HT5293 about XQuartz, which provides the functionality.

• Mail.app and Safari.app drop support for RSS Feeds.

One of the bigger-deal removals for some is the 'Web sharing' button in the System Preferences > Sharing tab that controls Apache. Apache is still there, and can be manually set up, but the old one-click solution is gone. That was one of the things I used to demonstrate to people new to the Mac that they found astonishing.

• Safari doesn't have separate source windows
• Calendar doesn't support scheduling scripts
• The option to disable smooth scrolling was removed
• The tab for installed updates was removed from the Software Update preferences
• Mail doesn't support notes
• Nested menu titles like >File>Duplicate no longer work in the keyboard shortcut preferences
• Old files cannot be locked automatically
• Safari doesn't have RSS buttons

Safari Changes:

Activity Window Missing:

Prior to Mountain Lion, there was an Activity window that could be opened from "Safari > Window > Activity". Now however, that functionality is no longer available. I found the Activity window to be especially useful for downloading videos from sites like YouTube. I'm sure there were many other uses for it, but that was what I primarily used it for.

Delete Button No Longer Goes to Previous Page:

In Lion, one could navigate to the previous page in Safari by pressing the delete key, but in Mountain Lion this feature is no longer active by default (in Mountain Lion it's Cmd[). However, you can activate it with this terminal command:

defaults write com.apple.Safari com.apple.Safari.ContentPageGroupIdentifier.WebKit2BackspaceKeyNavigationEnabled -bool YES