Cleric House rules in my game (think most of these have been mentioned before)
Domain spontaneity - (defintely adds flavour without being too overpowering)
Cloistered cleric as the baseline cleric - PHB cleric is only for the more martial faiths
'forcing' clerics to multiclass into faith specific areas - eg priests of martial gods have to take 1 level of fighter for every 5 cleric levels. ditto for gods of Trickery (rogues), Poetry/Music (bards), Nature (ranger/druid) etc. Crafting / Household gods would probably use levels of expert but i'd be sure to give a PC something extra (eg bonus feats) if they took an NPC class.
spell casting classes (eg gods of magic) don't get as much from this approach (other than massive spell selections..) but thats where a cloistered cleric with the right domains works better.
IMC at the moment,
Cleric 10 Fighter 2 priest of the god of challenges - happy to mix it up in the front line alongside the tank and the swashbuckler and with righteous might and other buff spells takes the lead when required. Cure Criticals on undead are impressive as well
Cloistered Cleric 11, priest of fire, luck and gambling (imagine prometheus elevated to divinity) - out blasts the wizard with fire spells from a distance and makes good use of mobility and battlefield control spells. Screams and runs away like a little girl if anything gets too close
very different approaches to combats, very different flavour, but no serious tweaking with the rules!
(I did talk to the players about restricting the base spell list quite severely, giving an additional domain and then turning them into a completely spontaneous class a la sorcerer but neither liked the idea! Since my next campaign will likely be Pathfinder based i'll hold back on more HR's until i've played through the changes to domain abilities)