So since most of the stuff I talk about on this blog are either computer techy things and anime related things this blog post seems like a good idea.Anyhow let's start from the weakest to the strongest ones.I will split them into programmers and security hackers.Also those here are only from the anime I have watched,and the ones I bothered to remember.
Bought a super computer he helped build with his students.Hacked the worlds strongest supercomputer with it and partly succeded.
Yoriko Yunoki[Battle programmer Shirase]:
Got pwned by the 2 bad guys so she had to call for Shirase's help.Still apparently she is a child prodigy security hacker.
Saitou Hideki[Battle programmer Shirase]:
Nothing but a comic relief sidekick to the bad guy.
Ose Rintarou[Battle programmer Shirase]:
The big bad of that anime.He was beaten so hard that dropped him down here.
She leans more towards a programmer but she has latent potential for security hacking.Her masterpiece was a world popular video game that was used to bring down the big bad.The only reason she was not higher on the list was because her competitors in the anime were just ridiculously too overpowered.However she still managed to leak a video feed behind the big bad's back which was crucial to reunite the good guys.
The big bad that outhacked Baggis.Generally he observes the whole world from his worlds strongest supercomputer.
Alice[Kamisama no memochou]:
A security hacker.She is able to hack every camera,bankpretty much whatever possible in the world.In fact she can hack those to such detail that she is able to solve actual crime cases with that information alone.She is also actively trying to supress wars,end the poverty in africa etc...
Mimi[Mnemosyne no musume]:
Her hacking abilities have proven to be very useful.No facility was safe from her.
Katsuyuki Kamiyama[Mnemosyne no musume]:
A developer.Called the modern Von Neumann.Revolutionised computer science.Outsmarted Mimi.
Definitely more a security hacker than a programmer.He did develop drivers for his and his friends inventions but that is probably all.However hacking one of the most secure computer environments in the world?A day of work,for him.Hacking it even further so they could use the Large Hadron Collider,even easier.
Motoko Kusanagi[Ghost in the shell]:
A security hacker.One of her specialties is hacking into other people(as far as I remember,still she was pretty awesome but my memories of her are kind of cloudy).
The laughing man[Ghost in the shell]:
Another security hacker.He does everything Motoko Kusanagi does except he does it twice as good as she does.No wonder she had trouble identifying him.
Masami Eiri[Serial experiments Lain]:
With him the guys that are seriously overpowered start.He is a programmer.He developed the internet protocole version 7.In it he also developed a way to transfer a human soul into the internet.He was the big bad in that anime and could hack people with the blink of an eye.
Lain Iwakura[Serial experiments Lain]:
A security hacker.She transferred her soul onto the internet.Took root privileges from Masami Eiri and did rm rf /home/Masami Eiri(to translate to non geeks she deleted him).
A developer who could as well be a hacker.He developed a augmented reality application which became a de facto standard(this is why you should not use closed source de facto standard programs :P )which he used to manipulate the world around himself.He also programmed his soul onto the internet.He hacked enough people to start creating a new world order.The reason why he is in front of the pair from Serial experiments Lain is that he even knew how to do a proper backup of himself on the internet :P .
Shirase Akira[Battle programmer Shirase]:
Although it is implied he is a do it all he is a security hacker.Once he touches anything electronic the bad guy is stopped.He once blew up the worlds strongest supercomputer with a cell phone.The only reason he is not higher up is because he is from a humor oriented anime.However there are not many more places higher up than him.Kudos to him.
A hacker who spent several years undetected or at least unharmed right by the side of Kimijima Kou and his superhuman mind puppet.However his reat al masterpiece was the fact that he developed an antivirus against Kimijima Kou,and all that is even more impressive if you consider the fact that he did not have to hook his soul to the internet to do so.
Yuuki Nagato[Suzumiya Haruhi series]:
Yep,a hacker.Or to be more precise an actual alien humanoid interface computer.She is very able to hack actual reality,time and space are her root privileges.
Keep in mind tha this is just made for entertainment and is in no way accurate,just my personal opinion.
[Update]Honorable mentions go to Kirito and Kayaba Akihiko,since I forgot to mention them.