Like probably most collectors I like my games to be in neat rows in alphabetical order. Not only will this make it easy to find a game, it'll also look good and orderly. Unfortunately there are always some games that are different.
1st example: Enemy Zero - Sega Saturn. I could just as well have taken Panzer Dragoon Saga or Riven in this case, because all three of them have the same box. These games come on 4 cd's and thus need a different box. I don't like it, but it's understandable and thus somewhat acceptable.

You can also see 2 Electronic Arts game on this picture. For some reason Electronic Arts games for the saturn came in bigger, more hideous boxes. They are bad for the manuals, since they just lie loosely in them, they are hard to clean and they are shiny I hate them.
2nd example: Mass Destruction - Sega SaturnThere are 239 saturn games with a black spine. There is 1 saturn game with a greenish spine. This is Mass Destruction. For absolutely no sane reason this game has to look different from the other games. Not only the color is different, the saturn text and logo isn't colored in either. It makes no sense.
3d example: Street Fighter the Movie - Sega SaturnAlthough Mass Destruction's box was in a differet color, the shape was at least normal. This can't be said for Street Fighter the Movie. This game came in a box similair to those of American Sega Saturn games. With one little difference; the front is connected to the rest of the box with differently sized holes. So if the hinges of this awful game break, you can't replace it with an American front, you'll have to find yourself a new Street Fighter the Movie box.
4th example: Mega Drive EA gamesEA's evil box policy didn't start on the Saturn, they were screwing up lines of boxes in the days of the Mega Drive already. For some reason all Electronic Arts games for this system have a big yellow bar on them, that coveres about half the spine. Even blind people realize this looks dreadfull.
5th example: F1 Racing - DreamcastThis game has the title upside down. I don't understand how something this stupid can have happened. I could of course put the box upside down to compensate, but then I'd still have something upside down. Stupid game.
6th example: Some Master System games[/b[
I don't have much Master System games, but I already have some that mess up my neat lines. Of course there's My hero, but that came on a card, so I can't really get mad at that. I can get mad at Master Games 1 and The New Zealand story though. Master Games 1 has a huge blue bar over the spine and New Zealand Story misses the grey grid lines. Not as annoying as some other game annoyances, but especially the Master Games box attracts way too much attention.

Those are my minor annoyances. Feel free to add games to this list yourself.