My method: Druids/clerics/etc ... have access to all PHB spells at the start. These are the 'common' spells known to all. Then, I design short lists of extra spells from alternative sources that are commonly known to certain faiths, sects or other religious organizations of which the PC is a member or is affiliated. Then, I give the players the lists of extra spells their PC knows. There may be multiple lists for the same PC. These lists may be as short as 1 spell, or they may have a fwe hundred spells on them. For instance, a cleric of Mystra in one campaign I ran had a list for being a cleric of Mystra, a list for being based out of a church in Waterdeep, a list for being a clerical member of a certain wizard's guild, a list for being a member of the city guard reserves, a list for being a member of the adventurer's guild and a list for being a member of the royal family.
Then, I allow these characters to add spells to their lists by studying new spells that they encounter or create. If a PC has an opportunity to study with another spellcaster that can cast a spell they do not know, or locates a scroll with one of these spells, they may spend 8 hours studying it and add it to their list (if they make a Spellcraft check DC 15 + 2 X level).
The net result:
Each priest ends up with their own specific spell lists.
All clerics of the same God develop similar, but distinct flavor.
I get to use all those extra spells from all the sources, without flooding a single priest with 3000 choices for a first level spell.