WARNING! CONTAINS SPOILERS!
1. Melena's love interest and Elphaba's heritage.
In the book, Melena says she may have been raped by a munchin, possibly causing her to conceive Elphaba. In the musical however, it is revealed that Melena had an affair with the wizard of Oz, who was Elphaba's father. in the book, the wizard of oz has absolutely nothing to do with Melena.
2. Frex's occupation.
Frex's job is that of a preacher/missionary in the novel, while in the musical he is a governor.
In the book, Elphaba is one of three children, and has a younger brother named Shell. In the production, Elphaba states she is one of two. (The other obviously being Nessa.)
4. Madame Morrible's expectations of Glinda.
In the musical, Glinda is scorned by madame morrible, who believes she is a unworthy sorceress. In the book however, Morrible notes that she weilds great power and potential.
5. Nessa's disability.
Nessa is best known to be wheel-chair bound, despite actually being able to walk in Gregory Maguire's version. In the book, Nessa's tragedy is that she was born with no arms, and is able to transport herself via her legs. (Although she has a few balance issues.) Considering the fact this is a show, however, the changing of this is understandable.
6. Nessa's religion.
In the book, Nessarose is a religious fanatic, who is devouted to Unionism. This concept was scraped in the play, and it is unsure what Nessa mark 2's beliefs are.
7. Nessa and Boq.
"Bossa" is considered a canon couple in the show, whilst in the book they have absolutely nothing to do with each-other.
Originally, Fyiero was a very different character. He was quiet and not particularly popular, and had no association with Glinda. He was a lot less flamboyant and shallow. And, was never a scarecrow either, and died before the end. This wouldn't be very acessible on stage, so the above was edited out.
9. Boq and Elphaba.
Boq and Elphaba are close friends in the book. On the contary, this was changed for the musical. Boq even comes to resent Elphie towards the end.
10. Doctor Dillamond.
In the book, Doctor Dillamond was actually murdered. Once again, this was not featured in the production, where he just gets fired.