I really thought that I didn't have a preference. I really thought that I loved all of my bishies equally. After commenting on the SH forum, I think I realized that may not be the truth...
For the uninitiated, I shall briefly define the terms used in the title: "seme" and "uke". In North America, you might translate them as "top" and "bottom", but that doesn't really do it justice. In the world of Yaoi there are some nuances that delve deeper into these definitions.
Seme: Yes, the majority of the time is the "pitcher", or the one performing the penetration, to get all technical and such. However, you can usually figure out who that is before the sex even starts, or if it is missing altogether, like in many shonen-ai stories. Essentially, the seme is the instigator, the assertive, confident character of the pair. He is the one who approaches the other. Traditionally, he is taller, and slightly more muscular. He gives off a cool air about him and often oozes "sexy".
Uke: The "bottom", or "catcher". He is the one getting fucked, to get all crude and such. He is usually identified by larger, doe-y eyes, shorter in stature, and mildly naive. Often, he is unaware of his sexual preference, and is often nervous at the prospect of loving another man. He is sexy in his innocence and often feminine charm. He is the "girl" in the relationship.
For the most part I find that within the stories, roles are defined purely by the physical, so essentially who "pitches" and who "catches", but in further analysis, there are several characters I have met who cross the line between both, but not because their position in sex has changed, only because their personality is unexpected.
As mentioned at the beginning, I thought I love both equally, and that it depended upon the story. As I tried to make my point, I slowly realized that I really do tend towards the seme. I like the ukes, often think that they are cute, but in a friendly, little kid kind of way. Semes, on the other hand, drive me to hard breathing and hash-marks on my face... Semes get me hot and bothered, in all the best ways. (o^_^o)
Do you have a preference?