It's very tough to choose, but there have been dozens of outstanding new monsters in 3E. Here's my Dirty Dozen.
Death Giants (MM3): Lots of flavor, and well-designed high-level foe.
Devil-Bound Template (Advanced Bestiary): The whole AB is an amazing set of work, but this one stands out for fitting the mythos of devils well, and really tempting players into evil.
Eladrins (MM and BoED): Fill a planar need, and work as good-aligned foes.
Flesh Jelly (MM2): An ooze that actually makes me go "ick". Shoggothy goodness.
Inevitables (MM and FF): Fill an important niche in the planes, and hey, they have fun obsessions that make them easy to use.
Midgard Dwarves (Frostburn): Closer to the real Norse dwarves of myth. Also, badasses.
Necropolitan Template (LM): Technically taken from the 1E true ghoul (Dungeon #70), but the makeover in LM is well executed and makes them easier to adapt to a wide range of settings.
Nimblewight (MM2): Very cool clockwork flavor, so I wrote them into a Dungeon adventure.
Nerra (FF): Excellent themed monster, wrote them into a WotC adventure.
Shadow Fey (Open Design): One of mine, and extremely useful. Planar and with a strong set of nobles and appropriate special abilities.
Urskans (Frostburn): Swiped from Pullman, but who cares? Fun to roleplay, and just not much like most other arctic monsters.
Zombie Angel (Open Design): An idea from Matt Forbeck that tends to freak players out. Alas, not publically available.
Honorable Mention: Rune Golem, Dragon 343. Because druids need to shout "Blood for my lord Odin!" more often.
I'm sure there's many more. 3E has given us almost all the good monsters from 1E and 2E redone, plus whole new swathes of monsterdom. Life is good.