Author's note: after I wrote this post I have found conflicting sources on the current Schellhas list of gods.
The ancient Maya gods are not well understood -- in colonial and later writings, 250 names have been written down as names of various gods. Classifying them is difficult due to the fact that the gods seem to have various 'aspects', depending on the situation, and in in the case of some gods are several beings at once. Also, regional differences in religion complicates figuring out which god was which. Because of this only a few gods have been classified by archaeologists.
Schellhas Classification System
Currently, a system is in place to help identify the gods. This system is called the Schellhas system. In 1904 a man named Paul Schellhas looked at the Maya codicies -- Postclassic Yucatan folding books --, and focused on what the gods looked like, what they were wearing and what they were holding. When he thought he had identified a god from the rest, he gave each different god he identified a letter of the alphabet. He also did the same with mythical animals he saw in the codices. While in some Maya writings there are gods referred to by name, archaeologists still use the Schelhaus classification system.
A List of Schellhas Gods
-- God A (called Cizin or Kisin) was a death god whose name is translated as flatulent one.
-- God B was Chac, most commonly known as the god of rain. God C is k'uhul, a god that represents sacredness.
-- God D is the god Itzamná, a creator god.
-- God E is the maize god who has at least two aspects, the "Tonsured Maize God" and the "Foliated Maize God".
-- God G is K'inich Ahau, the sun god.
-- God I is the moon goddess Ix Chel in her young form.
-- God K is K'awil -- who may also be Bolon Tz'akab and the mannikin scepter god -- who is associated with rulership, lightning and fire.
-- God L is a merchant god, who may have been worshipped during the Classic period.
-- God M is a merchant god, Ek Chuwah, possibly worshipped in the Postclassic period.
-- God N is a term used for two ways: the Pauahtun a four-part god who held up the sky, or another god.
-- God O is the moon goddess in her old form.
-- The identity of God P, whose form only appears in the Madrid Codex, has several theories concerning its identity.
-- God S is found in the Dresden Codex and may be a Hero Twin.
-- God U is found in Almanac 8 and Almanac 43 of the Dresden Codex, and is possibly related to God K.
-- God Y -- whose name may be Ek' Zip or Ah Uuk Yol Xip -- is a deer god.
-- God Z, found in the Madrid Codex, is a scorpion god whose name may be Ah Tzul.
Reforming the Schellhas Classifications
Since he created his lists, some of the gods that Schelhaus classified have been reclassified (and the list of mythical animals has been expanded upon). A god called god F is now understood to be three different gods: god A' (possibly a violent death god); god R whose name may be Buluk Kab (a god possibly connected with floods); and god Q, whose name could possibly be Lahun P'el (a god possibly connected to the idea of "termination").
What Schellhas understood to be one god -- god H -- is now known to be two gods: god CH and God H. God H might be a god of wind.
There are also other seeming gods, as the Hero Twins are depicted as gods. In some images there are two paddlers depicted as gods that are called by archaeologists "The Paddler Gods". One paddler, named by Mayanists as Old Jaguar Paddler, at the font and Old Stingray Paddler, another recently given name, at the back. Thought to represent day and night, respectively, Certain creation stories involve the Paddler Gods as setting up the Cosmic Hearth (Jaguar Throne Stone) in a place referred to as Five-First-Sky.
"Handbook To Life In The Ancient Maya World"; Lynn V. Foster; 2005
"Mesoamerican Mythology"; Graham Faiella; 2006
Missouri State University; MAYA GODS AND GODDESSES