Just taking a look over at the stuff sitting on my shelf, I see:
Video DVD (animation, previews, superplays, etc...)
Digital art book (DVD)
Bonus minigame (on a separate disc, never released separately)
Faceplate (Xbox 360)
Controller (standard like Wii Play, specialized like Guitar Hero or Super Scope 6)
I'm sure I could come up with a lot more if I poked through Japanese release lists a bit. I know I've seen sets that include stuff like shot glasses, clocks, t-shirts, and even panties before. It may not be feasible to actually categorize all these kinds of bonuses outside of "standard" things like manuals and registration cards. Free text fields for more esoteric stuff may be more suitable.
Also, what about pre-order bonuses? I've seen a lot of Japanese releases that include drama CDs or telephone cards with preorders, and I know that bonus download codes have become quite common in the last few years, often differing by retailer. Would those be catalogued separately from pack-in bonuses?