No, I think that is a good idea

. Homemade cards and gifts from the bf are a lot more special to me (and a lot of girls I know) than jewelry, etc., at least while I am still in college, so I think it is very cool of your girlfriend to ask you to "make" something. (And, although probably said in jest, if I was bought something that looks homemade even though I asked my bf for something homemade, I would be so disappointed. )
I was the lucky recipient of a "make" day a little while ago. Along the same lines as making a gift, my guy made me a tape of a bunch of cool songs that I liked (not sappy stuff though, and a tape so I can jog with it....plus tapes take more time than a cd). He made me dinner which was incredible because he doesn't cook at all, ever, so the effort was noted. Plus, my favorite, he volunteered at a local soup kitchen with me because we needed volunteers. Since he is super busy and volunteering means a lot to me, I really appreciated it.
All the ideas mentioned are quite good. As MTSUgirl mentioned, a homemade picture frame with BOTH of you would be a great idea as well as pottery, candleholders, vases, etc..... Also, I guess this is not homemade, but it is one of my favorite gifts. My bf gave me one of his favorite old t-shirts. Since I know how much he liked to wear it, it meant a lot to me that he gave it to me. (I don't wear it to class, but I will sleep in it.)
Really though, my suggestion would be to "make" her a weekend and let her make all the choices, possibly surprising her along the way with small homemade gifts or little flowers.
You are right. This is what girls do. But really it is not that complicated. Treat us well and show us that you care. Good luck.