I don't want to provide support for this anymore.
The application is bad.
It can't load massive images.
It can't zoom.
It can't load images with pointless zeroes.
The one thing I do like is the downloading feature. If you have a stable connection, and know how to use it, it's pretty good IMO.

Original post. Beware of terrible application

Manga Reader
v 2.0
It's like a thing that reads manga, except you're doing the reading.

About

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Warning: Spoilers inside!

Pretty much, it lets you read a comic/manga that's stored in a whole ton of image files on your SD card. Oh, and it can also download manga. Sometimes. If it works.
There's no zooming, so this thing is kind of bad. If you can live without zooming, maybe you can use this.

Instructions

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Warning: Spoilers inside!

Instructions for manga downloading is in a different section of this post.
Put your manga in the folder /Manga/. The manga folder is on the root of the sd card.
Each manga should have a different folder.
Ex: /Manga/NarutoChapter1/
Your image files need to be in a specific numerical order.
It goes like 1.jpg, 2.jpg, 3.jpg, ect.
It can have names like 01.jpg or 001.jpg.
(It can load png, bmp, or jpg. Png is very slow. I recommend jpg.)
You can have more sub directories in your manga folder. Like this:
/Manga/Naruto/Chapter1/
And..uh..that's about it!
A perfect example would be like this:
/Manga/Naruto/Chapter1/1.jpg
Of course, it would have 2.jpg, 3.jpg, 4.jpg, ect.

Controls

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Warning: Spoilers inside!

General Controls
Use the dpad to navigate menus.
Manga Reading Controls
Use the circle pad or the dpad to navigate the manga page.
Press R to go to the next page.
Press L to go back a page.
Press X while reading a manga to show the time and page on the bottom screen.
Manga Selector Controls
Press B to go back a directory.
Hold L to move quickly
Press A to select a manga/enter a folder
Press START to go back
Download Menu
Press A to change something.
Left and right can be used to change the chapter number, save file, and load file.
Press A on the chapter option to use the number keypad to change it. (Left and right can also be used.)

Options

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Warning: Spoilers inside!

Speed - How many pixels the page moves per frame when moving
Return - Where you start out in the page when you go to the next one

Changelog

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Changelog

2.0

• Removes green bar part of the green bar when using old 3ds to maintain frame rate.
• Less confusing file selector.
• Removed option for dpad to switch pages.
• Removed ability to type in your own prefix.
• Removed touch screen page moving. Whoops.
• File format and pointless zeros are now automatically detected.
• Code was completely rewritten.
• When entering a folder that contains chapters for a manga you've viewed before, you'll automatically select the last chapter you viewed.
• Number keypad which uses the touch screen.
• Hold L in file selector for quick movement.
• You can now press left or right to switch the chapter number on the download menu.
• Oh, looks like the program freezes if you enter an invalid manga name. Remind me to fix that. I already built the 3dsx and cia, so I don't feel like fixing it right now.

1.8.9.1 - Still says 1.8.9 in the actual application. Updates lpp-3ds.
1.8.9 - Multiple download settings save slots. Unlimited. Press left and right to change slot when on download screen.
v1.8.8 - Small stuff.
v1.8.7 - Number of pages now automatically detected. No more manual exiting. Removes two pointless options on the main menu.
v1.8 - There's now an option to check if a new update is available. Go to the Options and press "Check for updates." Press X while reading a manga to display a bar on the bottom of the bottom screen with the time in 12 hour time and the page number. This can now use pages of a size smaller than what the minimum page size was. This will now use the n3ds's power if available.Manga downloading is now possible! Read my tutorial in this post.
v1.7.1 - updated lpp-3ds, and index.lua is now inside of the .3dsx.
v1.7 - Saves options and a few other stuff.
v1.6 - New version of lpp-3ds. Fixes of infinite glory.
v1.5 - Page number is now saved for each manga!
V1.4 - Just made it so you start on the first element after entering a sub directory. Instead of the zero-th element.
V1.3 - Minor changes, allows page movement from dpad.
V1.2 - Adds support for pointless zeros.
V1 - Initial release.

How to use the manga downloading feature

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Manga downloading tutorial

Here's my text tutorial on how to use the manga downloading feature:

Warning: Spoilers inside!

First, go to mangareader.net and fine a manga you want. Click on it to go to the chapter list. The url should be something like http://mangareader.net/MANGANAME.. MANGANAME is usually the manga's normal name in all lowercase and with spaces replaced with "-". Memorize what MANGANAME is. Go into the download option of Manga Reader. For name, enter what you got before from the url, MANGANAME. Then all the other information is self-explanatory. You can also press Save Options on the manga download screen to save all the stuff you've typed. Then you can press Load Options later to load it all. So you don't need to type in long manga names again. When you enter the name for your manga, the path it'll be saved to will be automatically generated for you. It'll be /Manga/whatever_manga_name/chapter-x.

Here's my video tutorial:

Video tutorial

(Information is a bit outdated. Save folder and number of pages no longer need to be entered.)

Don't forget that when you type in the name, it's case sensitive. (Usually all lowercase.)

FAQ

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FAQ

Freezes after starting a manga

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Warning: Spoilers inside!

(This generally doesn't happen with manga downloaded using the manga download feature.)
All pages must be no more than 2300x2300.

The 3ds has limitations on how big a loaded image can be.
To fix this, resize them to make them a bit smaller.
That's easy. I recommend Fotosizer. http://www.fotosizer.com/Downloading.aspx

Zooming?
no, sorry.

Download

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Downloads

https://github.com/MyLegGuy/MangaReader/releases

The zip has a cia (Thanks to MarcusCarter) and a 3dsx.