Even with the power averaging rule, which I commented on the "Powers" area of the Profile's skeleton, some characters will still be far too powerful to be fair with the others. So, it is regretable, but I have to draw a line and limit some of them. Use Ctrl + F to search for the name of the game, anime or series to see if any limitation is listed for any character of it. It'll be constantly updated too, so check it out every now and then.

Code Geass
Lelouch and C.C. (or rather, the Geass users): The Geass is a very powerful ability: it can make any person obey a certain limited number of orders, and therefore could potentially unbalance the game. Therefore, I'll add these limitations:
1 - The Geass cannot kill another character. If the Geass user tries to kill another character using this power, the Geass will simply fail, but it won't deplete the number of orders you can influence that character with.
2 - The Geass cannot order something that would utterly embarass the other character personally. (for example, ordering a girl to strip naked is NOT allowed). However, if it will ONLY embarass the character professionally (like order a waitress to constantly drop her tray), it is allowed.
3 - The Geass cannot limit the person's free-will for a big amount of time. For example,.. if you want someone to help in your mission, you may order them to help you, but it takes their free will for a seriously long amount of time, and that's not fun for the other player. Thus, you cannot order someone to follow you for a very long time or anything of the sort.

All the limitations above can be overcome, as long as you get permission from the other player to execute any of these forbidden orders. Also, you can pretty much ignore these rules if you're dealing with characters that have no player behind them (those that are NPCs).

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Death Note
Light Yagami and Misa Amane (generalizing, ALL Death Note users): The Death Note is a notebook where you can write the name of a person, and that person will die as long as you keep its face in mind while writing the name. Thus, it is an obscenely powerful tool. I'll have a couple of limitations for it.
1 - The Death Note cannot kill a character that is being controlled by another player. This rule can only be ignored if the player of the other character agrees to have his/her character killed in this way.
2 - The Eyes of the Shinigami can see the person's true and full name, but if won't be able to show the time of death of that person. This is just to limit the player from inventing times of death for each other character and all.

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Touhou Project
All characters: It's fine to use the powerful spell cards of the game, but remember they all have a margin of evasion, so don't go making anything completely impossible to evade. Additonally, if you're playing as Utsuho Reiuji, you can indeed create colossal bullets, but accept that even those can be evaded... all in all, I guess this last bit wasn't needed, but it doesn't hurt to make your point twice.