Excellent point.
As of January 2012, Google changed application guidelines (not hard, fast rules -- guidelines) to depreciate the menu. Apps that follow the guidelines (use Google Play as an example) will show three dots in the Action Bar (usually at the top of the screen) for secondary things like settings. Anything outside of the main functions of the app, which should be included on the Action Bar itself.
When an app is not built to these guidelines, you'll see a three dot menu item. On devices like the Nexus 7, it's placed along with the on-screen buttons. On devices without on-screen buttons, it's put in the same place but with only one item (the three-dot menu) it looks like a black bar with three dots in the center.
When a device starts up there is a file that's read that tells the OS a little about the hardware. In this file you can define that the device HAS a physical menu key, or doesn't have one. WHen an app calls for a menu, it's displayed as described above, based on whether the device has a key or not.
The best news is that Google knows developers are ignoring this recommendation, so they are revamping things again with a new layout using a sliding panel from the left, like the one in the Android Central app. This was a big deal at I/O, to let developers know that the best looking apps will all be uniform with this new panel.