My votes :
Mainstream:
Thissaly from DC. She's from the "Sandman" books and has had her own books in the past. She (like other elements from those stories) has crossed over with Hellblazer and the like. When talking about uber-characters that is a "character" rather than a megaversal force she's #1. Doctor Manhatten is nothing to the level of power she displays at times. Gods (the same ones who mess with Wonder Woman, and show up to talk to Dream) are scared to death of her. She can play at the same level as "The Sandman" and company and is powerful enough to bind and do damage to enemies at that level.
Once in a book while searching for the weakness of a Tharmic Null (long story, it was sort oa joke) she found a spell that could literally collapse the pillars of heaven and hell (yet was insufficient to destroy a Tharmic Null, NOTHING can stop a Tharmic Null.. which is it's weakness, you'd have to read it... Lol).
Understand though, that despite the fact that she could probably destroy reality 10x over, she chooses to pretty much just sit around in her apartment, sip tea, and keep to herself. She hates nothing more than being bothered by well.... anything.
Darkseid, Doctor Manhatten, The Monitor/Anti-Monitor... they literally just wouldn't have a prayer. She just doesn't care about them. Destroy the world? She'll just go live the same mousy lifestyle in another world. Destroy the universe? there are other universes. Destroy the Multiverse? She'll go sit in a pocket outside of creation.
So basically the penultimate character of DC pretty much sits around minding her own business, unless something manages to slot her off.... she has a temper (a really bad one) but it's hard to upset her because she minds her own business so well.
Non-Mainstream:
Jenny Quantum and "The Doctor" from "The Authority". These characters are so powerful they need to come up with the most absurd ways of neutralizing them or simply have them not be around to tell stories. Neither character has ever really fully cut loose as their full potential. I however still remember Godhead Vs. The Doctor you had this psychic parasite who pretty much takes over the whole planet, has power based on every person on the globe feeding into him, and he's wiped the floor with The Authority (including Apollo who is basically Superman... he gets trashed a lot though). Eventually The Doctor deigns to show up and appears as a giant head: Godhead goes on about being a god, etc... the counter statement statement was basically "There is only one being this world has ever known that comes close to the concept of 'God'" He then eats Godhead like a tic-tac. One of the more WTF moments I've read in comics. Jenny Quantum is every bit as powerful as he is, and maybe more so (they fight to a standstill in Authority: Prime... though the setup is stupid).
Those two followed by "Max Faraday" from "Divine Right" though he might have been retconned out of existance, nobody seems to write about him anymore.
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The Long Analysis:
It's not consistant. To be honest with you when it comes to comic books it ends with "Omnipotent" in pretty much every universe, and truthfully which omnipotent being is the most powerful depends on the needs of the story. There are things bigger than like The Spectre, or Living Tribunal at various times. Right now Marvel has had characters like "Roma: Guardian Of The Multiverse" and of course "The One Above All" if your getting into supreme power.
Characters that are not intended to be taken seriously, like the entire Dragonball Z mythos (which is a huge genere send-up/satire despite having it's own mythology and consistincy), or say Squirrel Girl. Squirrel Girl for example is NOT overpowered really, but she beats characters who are that powerful specifically for it to be funny, when they show it, it usually amounts to her doing something absurd with incredible numbers of squirrels... and let me be honest, I think part of the joke is that people undervalue how much a "few thousand" of anything is. While beating Deadpool was mostly a quick thing (and people, don't forget Squirrel girl does have enhanced physical abillities above the human level despite being a joke character, she also has natural weapons and such of her own) I will use him as an example. If you have 10,000 squirrels advancing on him from every direction in a furry horde, jumping out of the trees, etc... he's toast. You could do it with 10,000 of anything. His teleportation doesn't have THAT great a range, and he couldn't get out of the sheer mass they would be occupying, and really when they covered him there would be noplace for him to go. He's not going to kill that many with sword, and doesn't carry that many bullets. Ideas like that are inherantly stupid (as was clogging all Doctor Doom's stuff with suicidaal squirrels) but also at the same time make a warped amount of sense, which is why it's funny. Squirrel girl isn't the same kind of humor/powerful as say DBZ..... and I seriouslly DO want her for DLC for Marvel Ultimate Alliance 2.
Superman isn't all that powerful really because of his drawbacks, truthfully it seems like 99% of the time the stories are as much about him overcoming his weaknesses rather than being "super". What's more even operating at full strength there have been characters who are more powerful than him. Doomsday is a poor example since he only killed Superman because Supes was Cocky, but say Darkseid is a guy Superman typically needs help to beat, and guys like Lex Luthor have come quite close to beating him in the past, putting him in serious jeopardy to create tension for the story. Heck I think Lex actually HAS beaten him in the past and wound up having to let him go.
Batman I consider overpowered because of bad writing, people have written stuff with him taking down characters that should have been far beyond him. I'm all for cheering for the underdog, but he typically has so much writer's fiat on his side that he takes it to a new extreme. You see Batman Vs. just about anyone, and pretty much guaranteed Batman wins or gets a "draw" that should be beyond him.
Most of the truely overpowered comic book characters that are consistantly at that level do not use their powers for psychological reasons or whatever. For example, way, way back during the time the Dinosaurs roamed the earth there was a Marvel villain called "Korvac" who was omnipotent. He wound up killing himself. He did this by downloading information from the computer of Galactus, and wielding the Power Cosmic. I believe it was mentioned that The Silver Surfer and Firelord potentially have that much power, it's just they aren't good enough at using it, and generally hold themselves waaaay back. This is like why during the whole Parallax/Green Lantern Vs. Silver Surfer crossover fight a lot of people were irritated because the Silver Surfer wasn't allowed to use his full power (which he basically never uses anyway). Sentry, Captain Atom, Firestorm, Doctor Strange, and a really maxxed out Green Lantern with the right artifacts are in the same basic catagory, but for whatever reason they never actually USE their power.
So basically the answer as to who is most powerful (at the end of this longterm rant) is simply who the flavor of the week is. For example in one horrendously written comic book Captain Atom was able to beat The Authority (or well, certain members, and the writers were on his side).
Who is most powerful today won't be tomorrow. I remember when "The Beyonder" was the most awesome thing ever. Sure Doom beat him with the power of Galactus, but he was just learning then. Later he dude joined The Avengers and abolished death from the universe... today he is defined as a third rate "immature cosmic cube".... which was not the original concept.
Then of course you can get into ridiculous arguements in DC if you decide to start getting into the whole "Sandman" thing (which is part of the DC Canon). The Spectre being absolutly irrelevent compared to the level some of these characters (the embodiment of universal concepts) play at. Please note my mainstream nomination in the short version before the - if you've read this far.
