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TowermadnessHD is the best that I have found for the "traditional" tower defense format.

SpacestationHD is a nice alternative version. You have to spider out with a space station to mine minerals from asteroids while creating a defensive field against invaders coming from all directions.

There is also a bloons TD game out there, but it is not a HD version.
 
I love tower defense games but for some reason I didn't like Tower Madness HD (luckily I got it when it was free for a day).

There are some great iPhone TD games(Sentinel and Sentinel 2 as an example) that play just fine on the iPad but for native games I'd look into:

Plants vs Zombies HD
Fieldrunners for iPad
Last Front Europe HD
The Creeps! HD
Zombie Attack! Second Wave XL (Woot support devs who give us Universal apps!)
Guns N Glory (haven't played this one yet but toucharcade seemed to love it)
Knight Defense HD (chess meets TD)
 
I would love to see Defense Grid - The Awakening come out for the iPad. It would be awesome as its the best TD game I have ever played.
 
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