My favorite happened when I first started using UTAU. When I told my friend I got the program, she told me she voiced an UTAU and I should try her out, Misora Haru. Loved her. Well, I wanted to conver "Cendrillon", needed a male, and I found an UTAU named Jero at the wiki. Liked his design, loaded him in and when I had them sing together...INSTANT OTP! I still love making Jero x Misora Haru covers today, and feel they have always been my best mixed.
My second would have to be, haha, Yami Yume x Teto Kasane. Yes, Yami is my UTAU, but interestingly enough, the pairing so far has received some love. It's funny as it was my brother's idea to pair them, he was like "Yami would look good with Teto", he does...and sounds good with her, too! And so I ended up shipping them as well, haha.