Dislike to like: Heian Alien is probably the biggest one. I thought it sounded like crap when I first heard it, then I warmed up to the chime section, then I warmed up to everything else, and I'd say it's my 2nd favourite extra boss theme now.
I'd really go with a lot of stuff though. I discovered Touhou through the BGM, and when I did that I listened to tons of stuff I didn't like. Then I started hearing the themes in the games, and a lot of stuff that didn't thrill me at first (History of the Moon, Hiroari, Green-eyed Jealousy to name a few) started to sound a lot better.
Like to dislike: I can't stand a lot of PC98 stuff outside of the game itself, all three of MS Stage 4 boss themes probably being the best examples. No idea why, I just don't like them anymore.
Other than that, not much. I know there are a lot of themes I used to love but now feel pretty meh about (Centennial Festival, Nuclear Fusion, Immortal Smoke) but I wouldn't say I dislike them.
Special mention to Luna Dial. Went from great in my "EoSD is awesome because it's the only one I've played" phase, to crap in my "EoSD sucks because it's too popular" phase, to above average in whatever phase I am now. <_<