Many of the top feats have already been mentioned. I'll try to propose some that haven't been said (I appologize if I missed anyone's post).
Improved Familiar
(imp or quasit if you want to be effective)
(monstrous spider if you want to be a silk maker)
(shocker lizard if you are a Mechanatrix)
(Celestial Familiar, lantern archon if you want endless continual flame)
Tireless (regional)
Fearless (regional)
Constant Guardian
Duitiful Guardian (if you want to be a bodyguard)
Lifesense
Daring Outlaw
Shape Soulmeld was mentioned, but I'd like to point specifically towards <Planar Ward> (with a minor shout-out to Pauldrons of Health)
Corpsecrafter
Nimble Bones
Bolster Resistance
Hardened Flesh
Tomb-Tainted Soul
Skill Focus: Knowledge (religion)
(if you like Pale Masters)
Inquisitor
(if you like thrallherds)
Stand Still
Hold the Line
Natural Bond
Quickened Spell-like Ability
Entangling Exhalation
Great Fortitude --> Poison Healer
Endurance --> Steadfast Determination
Insightful Reflexes (replaces dex for ref saves)
Are we including Dragon Magazine and WotC online feats?
Keen Intellect (replaces wis for will saves and some skills)
Extra Familiar (Dragon # 280)
Enspell Familiar (1-mile share spells)
Token Familiar (like figurine of wondrous power)
Wild Cohort (though if you already have an animal companion, the Extra Familiar mentioned above recommend an adaptation for animal companions)