A photo album, or a framed photo, with photos of you, and the people in your life, and your surroundings (eg. your home, your school, the view from the house etc.) Just to show her parts of your life. Even if you send her photos on the computer already, it'll still be nice, because it shows you've put some thought and effort into it.
Here's an ides: Make a video of yourself saying sweet things about how wonderful you think she is, your feelings for her, ect. Burn it to a dvd. Write little notes in your handwriting; cute love sayings, quotes, things you say to each other, ect. and throw those in too. As others have said, a teddy bear or a little stuffed animal is always a plus! If she had a favorite candy, go buy a bag and toss it in the box with everything else. You can add glitter or confetti to the mix as well for added adorable-ness, then to top it off, put a paper on top of everything that says "Happy Valentines Day to the best girl on the planet" (or something like that, you get the idea!) Do this, and suddenly you're the most thoughtful, cutest boyfriend in the world!