Obtaining event Pokemons/items/Pokewalker Courses exclusive to overseas
Wonderguard Spiritombs that are not used in competitive play
Getting out of dangerous locations such as Mystery Zone
To me, it seems that Nintendo's losing a fair bit of money by limiting distribution of event exclusives to certain areas. Incidentally, even in Japan people find it difficult to attend events because they're only held in a few perfectures(states). As an example, the newest and final Pokewalker course, Amity Meadow, was only distributed to people who got on certain Japanese trains, making it impossible for people in rural areas to obtain, let alone players overseas.
Sending hacked Pokemons over GTS to "unreasonable traders"
slight LEGAL tweaks in Pokemon stats (e.g. nature, ability...)
Making a copy of an encountered shiny to be used for display
These 4 are all things I've done to varying degree, and I will defend. The GTS has long been polluted with people asking for legendaries in return for their Bidoof. Isn't it better to rid the network of these unreasonable trades which would otherwise simply result in the trade being deleted? As for the items thing, I haven't actually used it exactly, but I did use a 9999BP cheat on my Diamond, the reason being that getting BP's in that game is too inefficient. Now that I have Heartgold, with four other Battle facilities and a Trainer House, I feel that I don't need to resort to AR for this anymore. The last two refer to examples like "this Male Ralts has 5 max IV's (0 in SpA) but has a Careful Nature instead of Adamant", and "a shiny Whismur Roared me on the same day that a Shiny Dusclops killed itself with Curse". I've had both happen to me, and I had already spent hours trying to breed that Ralts, too.
Wonderguard Spiritombs that are used in competitive play
Sending hacked Pokemons over GTS indiscriminately
Manufacturing perfect pokemon
I'm pretty sure I don't need to explain these...
By the way, Nintendo's already tried to sue companies that make cheating devices, but have failed on multiple occasions. Thus, under the law, cheating devices are perfectly OK.