Marth Debuted in Smash Bros.: The cast of the show first debuted in the West in the cameo in Air. It didn't take ADV too long to pick up the KyoAni version of Kanon, but the Toei version had been out for half a decade at that point.
The train station that plays such a big part in the story is modeled after Moriguchi station in Osaka.
Ayu's winged backpack wasn't actually supposed to be foreshadowing her nature; it just turned out that way. The director told the character designer to take the wings off the backpack because they might count as a spoiler, but later added the wings back on.
No, those two moments in episode two of Kyoto Animation's adaptation are not Suzumiya Haruhi references; they were in the original game. It is pretty funny, though, all things considered.
Shiori's favorite fountain is located in Tokyo's Showa Kinen park, which in real life charges a fee and thus can not be entered freely.