All of CLANNAD's main female characters had their own themes. The ending song of the anime, Dango Daikazoku, even goes on to have the same tune as Nagisa's eponymous theme music.
Worth noting that virtually all of the main female characters in Key/Visual Arts' visual novels feature their own themes, and there's even one for a male character. (Natsume Kyousuke from Little Busters!)
Non-animate things have leitmotifs, too. For an example, a song called Snowfield plays when it's snowing.
On the same topic, a few themes are used for any event filling a certain theme, such as Shining in the sky and The Place Where Wishes Come True being used for many of the Crowning moment of awesome instances, A couple of idiots and Meaningful ways to pass the time for many of the comedic plot development scenes, Sping Wind and To the same heights for plot development in general and Distant Years along with Town, Flow of Time, People for flashbacks
Each of the heroines in Maji de Watashi ni Koi Shinasai! gets their own, of course, and Yamato has one himself as well. Various remixes of the two ending songs and the insert song are also used sparsely, and to good effect.
Each girl from Symphonic Rain has two leitmotifs: an instrumental version of their insert song which is played in story and an instrumental version of their image song which plays during the credits of their route. Chris himself also has Rain in my Heart.
The protagonist's mother from Dra Koi has a leitmotif that is a military sounding chant of various moe terms including moe itself. Moe! Moe! Moe moe moe! She herself is not very moe at all.
Nearly. Every. Single. Character in Katawa Shoujo has their own theme. Ranging from the Jazzy-sounding "Ah Eh I Oh You" for the Nurse, the wacky "Out of the Loop" for Kenji to "Caged Heart" for Hisaonote This one is fairly rare and only plays during specific scenes. In fact it's easier to just list off the ones who don't: Miki, Nomiya, Yuuko, Akira, Hideaki, Jigoro, Meiko and Sae.
Her Tears Were My Light has a character theme for Space and another one for Nil. The lower part from Space's theme returns at the end of the happy ending theme.