Sometimes it has to do with the deck and cards in it, sometimes it's simply what someone had for dinner when they designed the deck. Other times the community thrusts a name on a deck.
Example: the HB archetype Foodcoats started when @Nordrunner created a heavily taxing HB deck, calling it The Redcoats, after the heavy taxation the English imposed upon the American colonies. That archetype fell out of favor, but was reborn when Global Food Initiative (GFI) was printed, as it gave the deck a viable 3-point agenda to run. Because of the GFI, people started calling it Foodcoats.
If there's any specific archetype names you were curious about, ask away! Otherwise covering them all would take pretty much forever.
Edit: Oh yeah, the thread you linked to =P So the Wyldcakes archetype is named so from the inclusion of the cards Wyldside (wyld, obviously) and the card Adjusted Chronotype. The Cakes part is derived from the flipping of pancakes on the Adjusted Chronotype art, and the card itself is often referred to as "pancakes." @Chill84 was "reclaiming" the name into CakeBoss partially because of the TV show and partially because he's a silly bastard.