1000!th post, not reply.
As this is an epic moment, I will post my votes:
Spoiler for Win:
1
Shana (SnS) Hinagiku Katsura (HnG)
Obvious. Not really. Poor Hina. 
2
Suigintou (RM) Yuki Nagato (SHnY)
Never really liked Yuki that much.
3
Nanoha Takamachi (NA) Tamaki Kousaka (TH)
Obvious.
4
Kyou Fujibayashi (CL) Tsukasa Hiiragi (LS)
Tsundere + Zettai Ryouiki
5 Mikuru Asahina (SHnY)
Nagi Sanzenin (HnG) Tsundere! I also don't find Mikuru especially moe.
6
Louise Francoise (ZnT) Rin Tosaka (FSN)
Tsundere + Zettai Ryouiki for both, but Rin has twin tails. But Louise still gets it.
7 Horo (SW)
Tomoyo Sakagami (CL) Mildly difficult, but Tomoyo is semi-tsundere.
8
Nayuki Minase (KN) Konata Izumi (LS)
Faito Dayo!
9
Chikaru Minamoto (SP) Souseiseki (RM)
Yuri > Dolls.
10 Konoka Konoe (NG)
Fate Testarossa (NA) Obvious.
11
Maria (HnG) Aruruu (U)
Meido-san!
12 Evangeline McDowell (NG)
Kotomi Ichinose (CL) Mami-chan + Ko To Mi.
13
Rika Furude (HNKN) Sakura Matou (FSN)
Epic win.
14 Nagisa Furukawa (CL)
Hanyuu Furude (HNKN) Ehh, had to choose Hanyuu because of Yui Horie power.
15 Alice Carroll (ARIA)
Mion Sonozaki (HNKN) I must admit that she is quite cute.
16
Fuko Ibuki (CL) Saber (FSN)
Saber is more GAR than moe.
17 Touka (U)
Kagami Hiiragi (LS) Bipolar + Pigtails.
18
Sakura Kinomoto (CS) Ayu Tsukimiya (KN)
Difficult, but seeing more CCS recently tipped it.
19 Yuno (HS)
Haruhi Suzumiya (SHnY) She's pretty cool.
20 Shinku (RM)
Matsuri Shihou (Sola) Matsuri > Doll anyday.
21 Eri Sawachika (SR)
Ayumu Nishizawa (HnG) Normal girl vs. Yui Horie tsunderekko? Ayumu for "I like 2-d Girls!"
22 Setsuna Sakurazaki (NG)
Mai Kawasumi (KN) Yukari Tamura.
23
Tamao Suzumi (SP) Konomi Yuzuhara (TH)
Tamao-chan!
24 Eruruu (U)
Shiori Misaka (KN) Sick girls turn me on for some reason.
25 Vita (NA)
Teletha Testarossa (FMP) She's so moe that she's even moe in the English dub.
26 Yue Ayase (NG)
Tsuruya (SHnY) Fang power dominates low-profile match.
27 Nodoka Miyazaki (NG) Yurie Hitotsubashi (KM)
ABSTAIN
28 Suiseiseki (RM)
Sakura-hime (TC) Hate-vote, but I'm assuming Sakura is at least somewhat like her original counterpart.
29 Tamaki Kawazoe (BB)
Ryou Fujibayashi (CL) Ehh.
30
Rena Ryuguu (HNKN) Kyon's Sister (SHnY)
Omochikaeri takes home that loli in a bag anyday.
31
Sayuri Kurata (KN) Chiaki Minami (M)
Ahaha beats the living fat ahoge type thing.
32 C.C.
Kiri Komori (SZS) Hikikomori beats Pizza Butt.
EDIT: Christ, I waited an hour and a half for this.