Deities and Demigods has rules for that.
You have to consider that not every pantheon is appropriate for that stuff: The grayhawk pantheon (standard D&D-Pantheon) or the faerûnian pantheon (Forgotten Realms) would not be fit to sponsor clerics of the whole pantheon, since it is a loose pantheon (they are in the same pantheon solely because they operate in the same area). The drow pantheon would be appropriate, too, since the deities all hate each other (or almost: Selvatarm and Lolth are in league). The elven or dwarven pantheon, on the other hand, would be fine.
You have to have an alignment that is a valid one for one of the gods (except, perhaps, outcasts on the fringe on the pantheon, like Abbathor of the dwrves or Set in the Pharaonic/Mulhorandi/Egyptian pantheon), take his domains from any of the gods (although nothing differing from his alignment), and choose one favored weapon from one of the gods.
Alternately, you could create a "meta-god" entry for the whole pantheon, listing valid alignments, domains and favored weapons for pantheon clerics, maybe differing from the individual entries (in the elven pantheon, for example, I'd ban chaotic evil clerics, for the pantheon as a whole is between good and neutral, and possible favored weapons would be longsword, rapier, and any bow, since that represents the elven way best. Domains would be chaos, good, war, protection, elf, magic, nature, but not things like time from Labelas, since that's not an elven thing)