The largest "Japanese Programming Madness" instance I can think of is Sigma Harmonics by Square Enix for the DS.
The game's font is non-standard and encrypted to the point that it's physically impossible to translate it, not only for the fans but apparently for distributors aswell, since the game was never released abroad nor was it attempted by anyone in their right minds, all because the perspective is Portrait and the font goes from top to bottom vertically rather then horizontally (as it should in Japanese, but still).
Check the ROM out - it's like it's black magic in .nds format.
Sigma Harmonics really isn't that big of a clusterfuck. The font is in the pretty common NFTR format and there is no encryption. There are tools to extract the archives (including the official tool from the SDK) so unpacking and repacking isn't a problem either. Sigma Harmonics had *some* oddities but not any of the ones listed.
Time for a little rant since it gets me every time people claim how impossible some game engines are.
There is nothing that makes games played in portrait mode any harder to hack than normal games. People seem to jump to the font as being a big issue but it really isn't one. To understand that you must understand what a font really is. Speaking strictly in terms of what the NDS can do, a font is a collection of images for each character that will be displayed on screen. To display the sentence "Hello, world!" it will require an image for each unique character in the sentence ("Helo, wrd!"). A font file on the NDS is a collection of the character images and sometimes includes some extra data such as the width of the character depending on how complex the format is.
Here's the font I used when I was messing with Sigma Harmonics to give you an idea about how the font would work:
When turned the same way you would turn the DS to play Sigma Harmonics:
No modifications needed to the font besides inserting rotated ASCII and/or remapping the characters to the normal ASCII range.
Next is the vertical text problem. Generally (I'm sure someone can find something that is weird) when you are displaying text on the screen you will have an X and a Y position. Those correspond go the coordinates on the screen. At some point in the game's code there will be a part that calculates the position of the next character to be displayed. Assuming the DS is being held in standard mode, a game with horizontal text it will be modifying the X position to move it left or right. A game that wants to write the text vertically will modify the Y position instead. Now if we want to think about this in portrait mode you just flip the axes. In portrait mode, if you want to display the text vertically you would modify the X position. To display the text horizontally you would modify the Y position. If the game is displaying text vertically in portrait mode then you just need to modify the code so it's modifying the Y position instead of the X position to display horizontal text in portrait mode.
The other problem is since the game displayed a border around all of the text, that must also be fixed. The frame itself is generated programmatically taking in the edge offsets and then filling in the rest. A pretty good rule to remember when dealing with games is "If it can be see it happening, it can be hacked". That includes things that you normally don't think of as seeing such as enemy AI. The difficulty involved ranges but if you see it happening, it can definitely be hacked. Everything the game uses to run must pass through somewhere at one point. All you need to do is find one of those places and trace it back far enough to find the code you want. Anything involving graphics is easier to find because you are guaranteed it will eventually end up in the VRAM.