Oh god, this is going to be hard...
Hmm...I actually had to make a list because there were so many possibilities and narrow it down. But, keeping in mind that I have not seen any of Buffy or Angel, here is my list in no particular order.
Simon Tam, because we're really alike and I just get him. He's so awkward and adorable and everything that I normally fall in love with in fictional characters.
Topher Brink, for pretty much the same reasons above. I honestly do not think I would've continued watching Dollhouse after the first few episodes if it wasn't for him. There was a lot of Echo and Paul, neither of whom I was crazy about, so Topher was really the saving character for me. I loved him as the funny character at first, but his moral struggle was a really interesting and well-done arc and I really enjoyed watching it, even if it tore my heart out at the end.
Malcolm Reynolds. He's just such so strong, character-wise and personality-wise. He has his own system of beliefs, but he's a very honest character in his own way. I really love his sense of humour and his loyalty....I feel quite differently about him than the others on this list (and most of the people who were on the longer list), but I definitely think that he's one of my favourite characters period, not just Whedon.
Thanks for asking, even if it was really difficult :P