I like the bonuses when they are something physical. Shirt, poster, key-chain, etc. It makes it feel like it is worth something, and still functional after I stop playing the game. Software unlock bonuses piss me off. Such as the armor and black hole generator in Mass Effect 2. Pre-ordering at gamestop was the only place to get it, and you got it at the beginning of the game. It's equivalent to the strongest weapon in the game.
Back to Ani's original question, I think it is a fair system when the additions are cosmetic (like a costume) or whatever. Just so long as it doesn't affect gameplay. Sure, it sucks that gamestop usually gets the better bonuses over Amazon and Steam, but they have been in the pre-order bonus market (in one form or another) longer than the others. I buy almost all my games at full price (lately I enjoy the stuff they cram into collector editions for even more money), so it is a nice perk when you can pre-order for a little benefit. There are enough random bugs in release-day games that the pre-order baubles make up for it a little bit.
On the other hand, I have gotten screwed once before by them. I pre-ordered Muramasa: The Demon Blade and they sold me the game, but never gave me the poster that was supposed to come with it because they didn't have it in stock. They gave me $5 off instead. I would have much rather had the poster.