Oh wow...this is definitely hard, because the more series I get involved in, the more waifus I find.
But, I suppose, here's my top 2:
Chii: She was my first waifu, and what really got me into anime/manga in the first place. I just found her to be so adorable, and I wished I could have taken her home and took care of her myself.
Mio: Gosh, what can I say? When I saw the first episode of K-On, she was the first character that really caught my attention, and she reminded me a lot of myself: Easily embarrassed and afraid of gory stuff, lol. I just imagine if she was real we would be able to relate to a lot.