Killer Instinct for the SNES also came with a special OST CD, though that might have been first launch (i.e. the only option originally) and as such wouldn't qualify I presume.
There is the super bomberman + tap bundle. The chrono trigger with t-shirt bundle Just because it didn't have "limited edition" pasted all over it doesn't mean it wasn't limited. I suppose as far as I remember the Lunar / puppet bundle is the first real milking of the LE cow as I can remember, in it's capitalist form.
The copy of 'Lord of The Rings' I had on the C64 (UK), came in a big box with a copy of the novel, and a map. I seem to remember a few editions of C64 games that came with stuff like that.