I mean, one is a terrorist driven by a combined desire to show the people of the world just how awful they really are, and to prove that society is a mere couple of simple steps away from total anarchy...
And the other is a big purple space titan, who wants to kill half the universe with some magic, glowing rocks, because hes worried about resource depletion.
I love me some epic superhero silliness, but come on...
The Joker.
Every single time.
All if the above is true, but I stil really struggle with this question, and as such I can't vote - really wish there were some other options ( tie, too different to compare etc.)
Nolan's conceptualization of the character, the look, the dialogue, his plan ( yes, there are a few conveniences and things that dont quite make sense) is just.....well, wow, it's magic !
Ledger's performance brings all of that to life, and 'mesmerising " is an accurate description.
However, Thanos feels very real, his motivations are understandable - he's a more developed character than the Joker, who's utterly evil and insane, Thanos has a tiny bit of goodness in him, which he's willing to sacrifice and the impact of that decision isn't lost on him. I lived that little scene at the end, after the snap, where he has the vision of child Gamora. She asks him what it cost, and ehen says "everything " you believe him.
I have to give a slight edge to the Joker, because until cgi improves significantly, a live actor is almost always more engaging ( Im thinking of XM Apocalypse, when I say almost, there they should have used cgi ).
Ultimately I feel that TDK and IW are such different films that they dont neatly fit into the genre - they're extreme ends of the cbm spectrum.
TDK is what Batman would be like in the real - ish world while IW feels like an epic superhero comic book story, played out in live action.
Tough to compare.