There were some minor rule changes (or tweaks) all throughout the books. You'd have to almost read completely through both books side by side to pick out the changes. Most of the changes I noticed are with classes, the purpose being to balance them better against eachother, but most of the changes are subtle and probably wouldn't jump out at you unless you compared a 3.0 book to a 3.5 book.
When the 3.5 first came out, I started going through each book to highlight the changes. I ran out of motivation about half-way through the Feats chapter. Most of the changes really are very small and subtle.