I'd recomend Morissons Invisibles/Marvel Boy/The entire JLA collection, JMS Supreme Power Collection,
Warren Ellis Transmepollitan, Planetary, and The Authority.
Mark Millers Powers and Wolverines Enemy of the State are brilliant, and to a lesser extent i'd recommend his Authority work.
Id also reccomend Garth Ennis Preacher.
For D.C. :
I'd recommend:
Kingdom Come (The greatest D.C. story)
The Stories of Alan Moore (The Superman and Batman work is sublime)
Day Vengeance Trade
Morisson and Waids JLA runs
Most of the Geoff Johns JSA is preety good
As is Waids Flash
Birds of prey is also highly recommended (Although i haven't read it)
Green Lantern Re-birth is also amazing
And Identity Crisis is the best D.C. book since Kingdom Come
And of course theres Frank Millers; The Dark Knight Returns
For Marvel :
Any of the Bendis Dare Devil work is amazing, as is his Powers collection
The 1st Runaways trades are out at the moment, as are Heinbergs Young Avengers trades (Much better than the other Avengers book)
Mark Millers Wolverines, enemy of the state is one of the best Wolverine books
Wheeldons Astonoshing X-men is good, although i prefer Morissons New X-men
Invincible is very popular, although i havn't got round to reading it.
Most of the Ultimate work is generally good, although id stay away from the FF4, and Darevdevil stuff.
If you want something a bit more classic, i recomend both the Infinity Gauntlet and The Secret Wars.