Normal enemies, as far as I can remember:
More than one game:
All sorts of fairies
Fuzzballs (Kedama)
Two types, the one with a few hairs only appeared in ESoD and PCB; the common hairy type first appeared in PCB Stage 1, and then become the second most appearing enemy of Touhou.
Crows
Appeared in MoF and SA. Same sprite, different types of creatures.
Yin-Yang Orbs
Appeared in SA and subsequent games.
Spirits
Appeared in PoFV, SA and TD. The spirits in each game are of a different type.
ESoD:
Stage 2 ice/bird/cloth things: I think PoFV clearly indicated those are spirits, since spirits can also take a bird-like shape in that game, but probably not everyone thinks so.
Patchouli's magic books.
PCB:
It's debateable that all Stage 3 "fairies" are in fact Alice's dolls, or as someone said, "the whole stage is Alice!"
IN:
The sprite for stage 5-6 enemies are fairy sprites with rabbit ears added. Again it's debateable whether those are real rabbits, or fairies cosplaying as rabbits. Given that rabbits shouldn't have wings, and fairies also did cosplay in PoFV Eientei stage, I'm leaning towards the later.
SA:
Stage 2 boulders.