Body part (typically hand or finger) as relation to size. Thumbling, Uglit es-Subaa (finger-joint), Sinziro (span, length from tip of thumb to tip of middle finger), Der Angule (one finger and a half), Planpougnet (handful). On the other hand, so to speak, there's the Ear-Like Boy.
Food as relation to size. Cecino (Chickpea), Cabecita de Ajo (head of garlic),
Mamesuke (Bean Boy), Gahan Polpetta (Meatball Gahan)
Those two are by far the most common naming motifs that I've found.
Half. Nciç, Nus’s’ ns’es (Half-a-halfling). This seems to pop up in North Africa.
Animal as relation to size. Kerza (sparrow), Koukoudessis (as small as a mouse), Boconono (weasel), Little Shell. Probably the rarest naming convention that I've found.
Other. The Little Devil, Boy-Man/The Little Spirit. Still descriptive, but can be random.
This website is based on my research into folklore. Home to the Thumbling Project, collecting different versions of Tom Thumb and Thumbelina from around the world.