There are several books in the series, I've read the first two -- The Eyre Affair, and Lost in a Good Book. While neither is Shakespeare specific, the Shakespeare references abound. Listening to the audio book in the car I almost had to pull over out of traffic when she got to the bit about the "Baconians", going door to door with their literature trying to convince people who really authored the plays. The existence of lost work "Cardenio" also plays a major role in Lost in a Good Book.
If you're in the mood for something different, and especially if you're a geek who hates having to bridge the gap of choosing either something literary or something science-fictiony, I seriously suggest you go check these out. They're heavier on the lit than the science, I'll admit - all the time travel stuff is pretty slushy - but the entire concept is just so downright silly and fun at the same time that they're great.