They're stored as uncompressed, raw samples. So you can import the whole ROM into an audio editor and just look at the waveform until you spot something that looks like samples. Tweaking around with sample rate, 8-bit/16-bit, and stereo/mono will eventually get you the perfect sample. Clipping out the sample is as simple as zooming way in. You will plainly see where other coding ends and the sample begins, etc.
Original Mac, Mac LC, and Mac II style sounds don't have samples that you can easily extract. The Mac LC sounds like it's sampled, and maybe it is, but it would at least require some reverse engineering to get it out.
There are all sorts of other cool little sounds hidden in ROMs that are kind of cool to find. For example, the 6100 and possibly others have a sound effect from Sonic the Hedgehog when you pick up a shield.
I have a pretty good collection of extracted and recorded sounds that far exceeds what's included in MacTracker. It's very interesting to see how low-fi the sounds are. The most popular sound, still used today, is 22.050 kHz!
Here are the ones I've gotten out so far (Recordings are indicated):
http://benboldt.spymac.com/startup.zip
Note that the Mac Plus sounds are pulled from an emulator, so they are possibly very accurate.