Well, it has to fit in the space. CRxxyy denotes the size of the battery, where xx is the diameter and y.y is the height, in those pesky metric units. So for example a cr2032 is 20 mm in diameter and 3.2 mm tall. For the metroid cart, this should just work right away. Of coure, you need to respect the polarity, however.
For the bleepbloop cart things get a little bit trickier, since it was not designed to use a CR2032 battery. You might even need a smaller size, say a CR1632. You'll want to solder one of the sides to a pad for mechanical robustness. For this, you'll probably want to connect the + tab to the bottommost terminal. However, only the top terminal (of the two soldered to the holder) is actually connected electrically to the rest of the circuit on bleepbloops. The other one is just an island pad. So you'd need to make a connection between the two pads using a thin wire. And you'd also need to connect the negative terminal of the battery to any ground point on the board using a jumper wire. For example the on in the microcontroller programming port. You also need to put some form of isolation around or under the battery to stop it form shorting to other things on the board. Heatshrink is not recommended, as the battery is sensitive to heat. Or at least be careful if you use it. PHEW.
Oh, or...
http://uk.rs-online.com/web/p/battery-h
s/2197954/