Damn, Nick. You basically wrote a wiki entry on the topic. As soon as I read the title I said to myself, "Pshh, Batman. No question." Spidey is in second in my mind as well.
I do have a bone of contention w/ your Top Tier Batman villains though. I think a good villain is not only the threat they pose to Batman and the world at large but the nature of their relationship to the hero. Mine would go from top to bottom as such:
Top tier/A-list villains:
1. The Joker - Yin to Bruce's Yang. Complete chaos where Batman is utter control. The speech Ledger's Joker gives dangling upside down near the end of the film The Dark Knight sums up their relationship beautifully.
1. Ra's al Ghul - I'd tie him for first place b/c he's an EPIC character whose philosophies and methods are so close to Batman's yet so far away. Plus there's the drama of Bruce is technically part of the al Ghul family now w/ Damien and Thalia, and the role Ra's is always trying to play as a demented father figure to Bruce.
3. Catwoman (Selena Kyle) - She may be a "dark hero" now, but classically speaking she's temptation personified. Neil Gaiman summed up their dynamic quite well in his 2-issue story "Whatever Happened to the Caped Crusader." Elseworld tales always having them "end up" together as Selena converting over to Bruce's side. But the whole point of Catwoman (originally at least) is that she cannot be taken over to the "good side" completely. Gaiman's tale portrays a more accurate ending for a Bats/Cats pairing, one in line w/ the character Frank Miller re-invented in "Catwoman: Year One."
4. Two-Face (Harvey Dent) - In the last 15 years or so he's been molded into more of a villain for Dick Grayson, aka Robin I, Nightwing, Batman III (Azrael was Batman II technically). However, I think he's a constant reminder to Bruce of his limited power and that there is evil waiting to be unleashed in all men, even the good ones. I'd put him below Catwoman b/c he doesn't pose as much of a threat the hero as she does.
5. Hush (Thomas Elliot) – He's such a threat because he knows. Everything. And in the comics he's currently pawning himself off as Bruce Wayne. He's poised to possibly be one of Batman's greatest villains.
6. Riddler (Edward Nigma) – Well, I would’ve made him #5, but all the awesomely evil-genius things he did in the original Loeb/Lee “Hush” storyline has been undone by putting him in a coma that wiped his memories clean. *groan* Of course it’s his superior (?) intellect that makes him top-tier. He found a Lazurus Pit to heal his cancer, manipulated Thomas Elliot, and basically just royally fucked w/ Batman in “Hush.” However, he is now (post-coma) a freelance detective. Despite DC’s desire to turn every popular villain into a hero, I still rank Riddler as one of the most dangerous members of Batman’s sizeable rogues gallery.
7. Penguin (Oswald Cobblepot) – I almost tied him w/ Riddler, but he’s just not as smart as Nigma. Then I almost lumped him in with the #8s, but decided he’s just too iconic to classify him as “interchangeable.” Currently in the Bat-books Cobblepot does use his intellect to remain “legit” in Gotham and stay clean enough to keep out of prison (or manage to escape when he is caught/convicted) However, he is a major—if not relatively quiet—source of Batman’s problems by greasing the wheels that allow criminals to operate in Gotham. The only thing with Penguin is that in the comics seemingly anyone can come in and be the next “big boss” so his personal threat level isn’t truly all that high.
8. The following villains are fairly one-note (i.e. gimmicky) and can all be interchangeable for this slot depending on the story/context in regards to their threat level to the hero.
Poison Ivy (Dr. Pamela Isley) – mind control through her manipulation of plants makes her a formidable adversary but she’s limited in her motivations
Scarecrow (Dr. Jonathan Crane) – Connection to Arkham, fear gas and variations thereof are almost always easily thwarted.
Mr. Freeze (Dr. Victor Fries) – Dramatic backstory; cool costume; freezes stuff, which can suck.
Killer Croc – his invulnerability & superior strength as well as almost sympathetic backstory make him a worthy top-tier foe
Clayface – The reason he/she/it (depending on which of the five versiona you’re talking about) belongs on this list and not the 2nd string squad of villains is it is can be very dangerous because of the unpredictability of his moods/motives and of course it’s a freakin’ shapeshifter.
2nd stringers/JV squad
Red Hood/Jason Todd - Robin II resurrected and pissed off. I’d put him in the top tier, but he can’t make up his mind if he’s a bad guy or not (he doesn’t mind killing, but they’re villains he kills). His instability makes him dangerous to the Bat-Family nonetheless.
Club of Villains (Grant Morrison) – Morrison tried to make an indelible stamp on the Bat-mythos by having this group of European 2nd-stringers turn Batman crazy thus leading to his “Death” in Infinite Crisis. The real villain is Morrison’s piss-poor story/writing.
Solomon Grundy – more or less a DCU villain now than a Bat-villain; he’s getting a revival and re-boot w/ all the Infinite bollocks going on in DCU currently; seemingly immortal, big-ass zombie-like-guy
Lady Shiva – World’s greatest martial artist; now a “top tier” Robin III/Red Robin villain.
Deadshot – DCU’s #2 guy w/ a gun. I always confuse this guy w/ Deathstroke (who’s #1 w/ a gun and a Teen Titan/JL villain).
Harley Quinn (Dr. Harleen Quinzel) - A glorified henchwoman to the Joker (so she’s dangerous by association) when she’s not roommates w/ Catwoman & Poison Ivy (I’m groaning at you, Gotham Sirens), but a fun character.
Bane - dangerous, but not much more than a roided-up douchebag.
KGBeast – Russian assassin; is still taking the end of the Cold War pretty hard
Man-Bat (Dr. Kirk Langstrom) – Pretty self explanatory, a man that turns into a giant bat. Kinda like a werewolf that flies.
Mad Hatter (Jervis Tetch) – neuroscientist that developed a device for mind control; pervy lil’ dude.
Black Mask – crime boss who was out to get Bruce Wayne
Ventriloquist - mob-boss that talks though a puppet named Scarface dressed like a ‘40s gangster; original was an old guy and the new one is some chick.
Mr. Zsasz – Serial killer; keeps slash marks on his body for all his victims
Firefly (Garfield Lynns) – pyromaniac; likely teased mercilessly as a child for having such a ghey name.
Maxie Zeus – crime boss; uses a glorified cattle-prod to shoot electric “bolts”
Anarky – Teenage anarchist that’s not even a Batman villain anymore; he’s now relegated to tormenting Robin III, Spoiler, Huntress, etc.