My thoughts on the results:
1 Reimu Hakurei 6430 23.5% 3.95% 827 Expected, but I kinda find her overrated.
2 Koishi Komeiji 5992 20.56% 3.68% 801 I like her, but THIS high, wow!
3 Marisa Kirisame 5895 23.33% 3.62% 778 Like her more than Reimu but still kinda overrated.
4 Flandre Scarlet 5311 23.57% 3.26% 705 PRIME EXAMPLE OF OVERRATED CHARACTER HERE!
5 Alice Margatroid 5271 28.45% 3.24% 613 She's a interesting character, but not my favorite.
6 Sakuya Izayoi 5171 26.37% 3.18% 657 Finally, someone I actually like!
7 Remilia Scarlet 4854 23.21% 2.98% 615 Overrated, not much more to be said.
8 Aya Shameimaru 4630 26.64% 2.84% 632 SHAMEIMARU!
9 Satori Komeiji 4270 19.04% 2.62% 476 I like the SA characters more, but Satori's cool.
10 Sanae Kochiya 3960 27.12% 2.43% 457 Just this......:
http://www.youtube.com/watch?v=QFEkBu9RDgA11 Youmu Konpaku 3854 29.49% 2.37% 474 I character I love, alot.
12 Yuuka Kazami 3782 24.15% 2.32% 435 I keep getting reminded of her creepy antics in fandom, *gets chills*.
13 Yukari Yakumo 3670 23.98% 2.25% 441 :3
14 Hata no Kokoro 3550 9.23% 2.18% 580 More creepy than cute (Especially with those masks), and bland. NOT A GOOD CHARACTER TO ME.
15 Fujiwara no Mokou 3463 25.26% 2.13% 409 BURN BABY BURN!
16 Yuyuko Saigyouji 3322 27.37% 2.04% 388 The lovable and motherly fatass.
17 Tenshi Hinanawi 3245 19.35% 1.99% 429 :3
18 Patchouli Knowledge 2843 21.54% 1.75% 341 I like Koa more.
19 Hong Meiling 2764 28.81% 1.7% 338 Interesting character to say the least.
20 Momiji Inubashiri 2612 21.56% 1.6% 367 I think Kagerou did the wolf youkai idea better, sorry.
21 Byakuren Hijiri 2556 16.51% 1.57% 315 The Arceus of Touhou, really.
22 Nitori Kawashiro 2524 21.74% 1.55% 362 I like Hina more, and that FUCKING Funi video about her V-V.
23 Utsuho Reiuji 2492 18.04% 1.53% 318 :3, needs to be higher though.
24 Ran Yakumo 2324 27.03% 1.43% 304 Yukari's Shikigami. Loyal guard and obessor of Chen.
25 Kogasa Tatara 2313 14.96% 1.42% 322 I don't care for her, AT ALL.
26 Mononobe no Futo 2301 11.82% 1.41% 341 See Utsuho
27 Toyosatomimi no Miko 2183 14.69% 1.34% 299 See Kogasa
28 Eiki Shiki, Yamaxanadu 2159 25.89% 1.33% 273 MY FAVORITE CHARACTER FROM MY FAVORITE TOUHOU GAME!
29 Reisen Udongein Inaba 2094 19.17% 1.29% 252 See Futo
30 Rumia 2000 26.45% 1.23% 268 Cute, but creepy. Funny, but somewhat horrifying.
31 Parsee Mizuhashi 1969 21.33% 1.21% 255 She's boring boring very very boring........
32 Suwako Moriya 1950 19.71% 1.2% 243 Cute as hell, curious and quirky.
33 Cirno 1895 28.32% 1.16% 293 The du.......I mean strongest!
34 Iku Nagae 1850 16.51% 1.14% 279 FEVER!
35 Nue Houjuu 1848 10.62% 1.14% 251 See Parsee
36 Kaguya Houraisan 1775 24.76% 1.09% 228 NEET X15!
37 Hina Kagiyama 1621 23.52% 1% 170 SPIN SPIN SPIN! Needs to be higher.
38 Keine Kamishirasawa 1567 19.44% 0.96% 185 The were history eraser!
39 Nazrin 1501 14.5% 0.92% 186 Hey, Rat, can't you be more interesting to me. And if you can't tell, UFO is my least favorite Windows game.
40 Kasen Ibaraki 1450 12.37% 0.89% 188 I haven't read the manga, so don't know
41 Mamizou Futatsuiwa 1434 7.78% 0.88% 222 :3
42 Renko Usami 1414 17.3% 0.87% 181 She only appeared on a freakin' CD! What's so interesting about her?
43 Rin Kaenbyou 1375 15.63% 0.84% 211 Hell kitty! I love her.
44 Suika Ibuki 1369 17.65% 0.84% 176 I like her, druken oni.
45 Seiga Kaku 1335 11.81% 0.82% 181 I like the other TD characters more, but Seiga is cool.
46 Mystia Lorelei 1299 19.48% 0.8% 209 Yuyuko's bait. Song bird!
47 Shou Toramaru 1294 21.26% 0.79% 169 Sadly my favorite UFO character. A wild cat youkai is a nice idead TBH.
48 Daiyousei 1289 18.73% 0.79% 180 Cool fairy.
49 Komachi Onozuka 1209 14.98% 0.74% 152 I prefer her boss, but I still like Komachi.
50 Kanako Yasaka 1133 19.94% 0.7% 144 A nice idea, but a weird execution.
51 Ichirin Kumoi 1075 19.51% 0.66% 152 See Sanae.
52 Yuugi Hoshiguma 1067 14.98% 0.66% 159 See Suika.
53 Hatate Himekaidou 969 8.7% 0.6% 158 I prefer Aya more. All I need to say.
54 Chen 934 18.51% 0.57% 140 CHEEEEEEEEEEEENNNNN!
55 Minamitsu Murasa 901 15.46% 0.55% 117 Captain, can't you be as good as you are in the Littleshrimp comics?
56 Kyouko Kasodani 897 8.17% 0.55% 146 I like her, cute as fuck.
57 Shizuha Aki 855 12.31% 0.53% 128 I'm surprised, really.
58 Eirin Yagokoro 845 16.33% 0.52% 101 She's a cool nurse, really.
59 Koakuma 837 15.49% 0.51% 120 Koa being this low is a travesty.
60 Yamame Kurodani 814 16.42% 0.5% 113 Needs to be higher, one of my most underrated Touhous to me.
61 Minoriko Aki 800 10.75% 0.49% 123 See Shizuha
62 Rinnosuke Morichika 795 35.25% 0.49% 119 See Ichirin.
63 Tewi Inaba 776 14.47% 0.48% 117 The lowest IN character. Surprising.
64 Yoshika Miyako 718 8.57% 0.44% 87 Being her master, nice Zombie character.
65 Soga no Tojiko 704 7.13% 0.43% 91 She's no Mima, but it is a interesting character anyways.
66 Maribel Hearn 701 7.66% 0.43% 103 See Renko
67 Lunasa Prismriver 677 18.9% 0.42% 87 Needs to be higher.
68 Medicine Melancholy 628 21.59% 0.39% 94 I don't care for this one all that much.
69 Yumemi Okazaki 615 13.72% 0.38% 104 Badass redhead.
70 Hieda no Akyuu 614 20.86% 0.38% 83 See Nue.
71 Wriggle Nightbug 562 36.73% 0.35% 74 I understand, but I like her...............
72 Letty Whiterock 549 25.5% 0.34% 86 *Insert fat joke here*
73 Kosuzu Motoori 448 5.16% 0.28% 92 The retro Komachi!
74 Shinki 444 8.74% 0.27% 73 YEAH! Needs to be higher.
75 Mima 433 13.58% 0.27% 83 See Shinki. I have a soft spot for this forgotten character too.
76 Luna Child 364 7.17% 0.22% 56 See Wriggle
77 Watatsuki no Yorihime 346 10.8% 0.21% 60 Badass swordsman. Needs to be higher.
78 Star Sapphire 339 14.22% 0.21% 64 See Luna Child
79 Lily White 322 22.53% 0.2% 45 IT'S SPRING. NOT NOW.
80 Lyrica Prismriver 301 23.46% 0.18% 45 See Star Sapphire
81 Sunny Milk 285 16.18% 0.18% 50 So fuckin' adorable :3.
82 Alice's dolls (Shanghai, Hourai, Ooedo etc.) 260 11.04% 0.16% 45 I love these little buggers.
83 Unnamed book-reading youkai (Tokiko) 259 12.74% 0.16% 38 See Yaname.
84 Gengetsu 252 22.7% 0.15% 45 God Fairy, YEAH!
85 Merlin Prismriver 246 11.03% 0.15% 44 My least favorite of the Music trio.
86 Kisume 234 19.85% 0.14% 34 Bucket loli.
87 Watatsuki no Toyohime 176 13.51% 0.11% 31 Needs to be higher.
88 Unzan 168 7.5% 0.1% 44 BRO FIST!
89 Yumeko 117 10.67% 0.07% 8 Red dress maid. Cool.
90 Mugetsu 114 11.94% 0.07% 20 Okay to me.
90 Kana Anaberal 114 16.18% 0.07% 18 See above.
92 Mai 101 9.38% 0.06% 16 Fuckin' cool.
93 Reisen 94 17.31% 0.06% 20 See Kasen.
94 Chiyuri Kitashirakawa 85 5.08% 0.05% 12 The cousin of Murasa and Nitori. Not much more.
95 Kurumi 79 3.57% 0.05% 11 Needs to be higher.
96 Elly 77 10.64% 0.05% 15 Needs to be way higher.
97 Fairies (fairy maids, sunflower fairies etc.) 73 23.91% 0.04% 27 See the dolls.
98 Kedama 67 6.38% 0.04% 11 FOE!
99 Youki Konpaku 64 9.76% 0.04% 16 Don't care.
100 Layla Prismriver She didn't even appear in an official Touhou media!
My thoughts on the Top 100. May be biased, but whatever.