My NPCs, anyway, don't use many metamagic feats (it's kind of a pain in the butt to prepare) but an easy one like Energy Substitution rules the school as far as I'm concerned. Also use Extend Spell for a Mage Armor or Haste that just won't quit.
Silent spell is VERY important when you're trying to rain death down on a group of baddies from a hiding place without giving away your location. Silenced hold person and sleep spells are also very useful...
Actually, I believe no one has ever used (or taken) a Metamagic Feat...
If I had to choose a Feat, I would take Extend Spell or Energy Substutition (Since Energy Substitution requires another Metamagic Feat, I would have to take Extend Spell first... )
Feats that my groups have used..
Heighten ( Most people in my group take this one asap, to each his own eh? )
Still (The fighter/wizard loves this one)
Silent (Ditto for the rogue/sorcerer)
Energy Substitution ( A fav of mine personally)