And why?
Comic books, TV series, cartoon, and movie.
Since I suspect that the Joker will get a lot of votes, in that case who is your second favorite?
Joker sucks. 
(Well, no, but he’s way overused.)
Me, I’m a partisan for the Riddler - comics and DCAU versions. Gorshin and Carey’s versions are OK, but really not the same character. Kinda pissed off that he’s being revillainated…or appears to be. It’s hard to tell what the hell Daniel’s doing since he hasn’t actually appeared save for the arc that seemed to unredeem him, and one where he may or may not have been the villain. I was also annoyed at his jobbing for most of his time as a good guy, and REALLY annoyed at the story that presented him as cheating in his detective role, but that’s a problem with a lack of respect for the character, not a problem with the premise of him going straight. I do tend to ignore the ‘I can’t help myself!’ explanation for his riddles, and just assume he’s a brilliant, if dishonest, man who is pitting himself against another brilliant man.
Also fairly fond of the Scarecrow. Partially for the visual, partially for the obsession with fear - and especially his own inability to feel it feeding that obsession.
I also enjoy Ra’s al Ghul’s attempts to mold Bruce into an heir.
I’ve read approximately two DC comics in my life, but Ledger’s Joker was awesome. I don’t think he did anything the entire movie that wasn’t awesome.
The Scarecrow from the first movie and Arnold’s Mr Freeze were also fun, in their own ways.
So excluding the Joker–
From the comics, I like the Scarecrow. I always thought he was one of the creepier and scariest villains.
From Batman:TAS my favorite was Clayface. HIs story was tragic and his “powers” were pretty cool.
Catwoman by a whisker. Second place goes to Oswald Chesterfield Cobblepot.
They’re all good, classic villains, but Batman has been running way too long.
He’s the Homer Simpson of comics.
After the Joker? Catwoman.
My favorite character from the 90s cartoon is Mr. Freeze, though I also like the Riddler a great deal. In the Nolanverse, Two Face and Joker were both fantastic.
I don’t read the comics and try to forget every other movie before Batman Begins.
What? I personally dislike the character of Batman a great deal, but comparing him to Homer in any way is pretty ridiculous,=.
The Bruce Timm and Paul Dini animated series made just about every villain shine. Their tragic Mr. Freeze was a very notable showing. Even their Clock King was great.
I keep thinking of BTAS and thinking The Clock King would make a fantastic film villain based on his ability to speed up or slow down time.
Having never been a fan of the comic books and cartoons (unfortunately), I have only the filmed versions to go by. Having said that…
More than OK. They’re my favorites. I love that skinny, weird, almost sexually perverse character with the silly maniacal laugh. Carrey did a good job too.
I’d have to see John Astin’s portrayal again, but I remember not liking it very much.
Joker first, of course. I don’t know who I’d rate as second, but the Riddler has the most unused potential - he’s generally portrayed as an goofy idiot who compulsively sows the seed of his inevitable capture in every crime he commits. In real life, criminals who taunt the police (Zodiac, Beltway Sniper, Unabomber, etc.) are terrifying. Instead of a compulsive jackass who can’t help himself, portray him as a genius level, malevovlent, deeply narcissistic psychopath who taunts the police and Batman to prove his own intellectual superiority and you get a much more interesting character. I’ve only caught it a few times, but the Riddler from the new “The Batman” animated series seems to work pretty well on these lines.
The Riddler
Frank Gorshin was related to a classmate of mine. Got to meet him.
It’s a toss up between The Joker of Killing Joke/Death in the Family, and Two Face of The Dark Knight Returns.
Pretty much for the same reason - they both represent the other side of Batman, and how he might have turned out had things gone a little differently. Which of course is why I prefer Batman to Spiderman or Superman, who are just annoying prissy wankers. Unsurprisingly, I’m a Green Arrow fan too.
Scarecrow. Fear is supposed to be Batman’s weapon; I like how the Scarecrow turns that around on him.
My first introduction to Batman was via the 1960’s TV show when I was a kid. From that standpoint, it’s Catwoman by a mile.
Julie Newmar in that outfit made me feel things I didn’t yet understand.
Joker’s number one. He represents chaotic evil in opposition to Batman’s lawful good.
Catwoman’s in second place because of the sexual tension.
Ra’s al Ghul’s in third place because he’s interesting for his own sake rather than because of what he represents to Batman.
King Tut. If only because the choice emphasizes which Batman I consider to be THE authentic one.
I had read some things about the plan for the sequel to “The Dark Knight” movie. Apparently it was supposed to have Johnny Depp as the Riddler and used pretty much in the way you just wrote. The problem with that being that the Joker was already like that in “The Dark Knight”. Joker kind of stole both Two Face and Black Mask’s MO in that movie.
For me it would be Joker first, he is simply the best supervillain ever created.
After that, hmm, I like Two Face but he is often not very well characterized (that is writers seem to focus on a two obsession when it’s all about a Jekyll/Hyde character sharing the body at the exact same moment). Scarecrow is great, but they never play him up to his scary potential. I only know Black Mask though “The Batman” cartoon, but there is an episode with him where he is locked up in Gotham precinct’s cell and his organization tries to rescue him that is really awesome. It kind of foreshadows a bit of the plot of “The Dark Knight”.
I’d go for Black Mask, if only because I think he would be an awesome villain for the next Nolan/Batman movie.
Calendar Man.
Seriously, he was never a major threat, but his particular obsession made it a fun puzzle for a reader to guess what his next step was, but a little easier than the Riddler.
The only time I’ve liked the Riddler was the way Chuck Dixon portrayed him during the “Knightfall” saga. Every line the Riddler said was phrased as a question. I thought that was great, but neither prior nor subsequent writers supported this personality quirk of his.