The recent Player's Guide to Faerûn and Races of Destiny introduces Initiate Feats. These feats are similar to domains in that they grant a special ability but where they differ is that the Initiate Feat adds spells (usually deity specific) to a character's spell list rather than a bonus spell. Some are deity specific, others are for groups of deities.

It does provide some insight on how to further make clerics thematically aligned to their patron deity without necessarily resorting to a prestige class.

Here is an example of an Initiate Feat from Player's Guide to Faerûn:

Initiate of Nature [Initiate]

You have been initiated into the greatest secrets of Eldath's, Mielikki's, or Silvanus' church.

Prerequisites: Cleric or druid level 5th, patron deity Eldath, Mielikki, or Silvanus.

Benefit: You can rebuke or command animals or plant creatures as an evil cleric rebukes or commands undead. You can use this ability a number of times equal to 3 + your Charisma modifier.

In addition, you may add the following spells to your cleric or druid spell list:

3rd level Mold Touch
4th level Briartangle, Thorn Spray
5th level Fireward, Tree Healing