Jaiman is more northerly (the far north is Arctic) and was once a grouping of various kingdoms, most of which are now gone. There is still one relatively stable kingdom left (the Rhakhaan Empire), so that is a good starting spot for characters. Also, more modules were released for Jaiman, so some regions are well documented (e.g Rhakhaan, Tanara, Xa-ar, Norek, Aranmor).
Emer is larger and more southerly and has full-on jungles and desert (together with more temperate regions). It was once a single empire ruled by Titans, but is now a collection of various states, quite a few of which are stable (Sel-Kai, Kaitaine, etc.). Emer is less fleshed out by modules, but also has a bit more thematic variety (e.g. the Japanese-inspired Nuyan Khom, the Mayan/Aztec inspired Lankanok, etc.).