To be brutally honest, the second season of this show (the one preceding this one) will most likely be viewed as the funniest of the bunch, as the show was still incredibly fresh and the writers still had a large bank of ideas from which to draw on. Season Three, while still incredibly funny, didn't have quite the extra "oomph" that the second season had (what with the incredible Jim & Pam romance). That being said, after finishing this third installment of the show, I actually have gained even more respect for the writers and actors, as they didn't fall into the "same old, same old" trap of many comedies and instead kept right on developing the characters we have come to know and love.
The biggest change, of course, is the separation of Jim and Pam. As the third season opens, Jim has taken a position at the Stanford branch of Dunder-Mifflin (away from "beloved" Scranton) to try and escape the awkwardness of the Pam/Roy relationship (which begins to experience trouble of its own). This move, while losing the playfulness of the interactions of those two characters (which I consider to be the backbone of the entire show), actually serves to give the show more credibility, as you will be pulling even more for the couple to be re-united (whether or not that actually happens is for you to find out!).
Another curveball from the previous season is the development of characters from the Stanford branch. While season two essentially takes place almost exclusively inside the Scranton office, this season spends a considerable amount of time following Jim as he meets and interacts with his new co-workers. Again, this may not be what you want to see in the short-term, but it eventually serves to give the show an even stronger base of characters in Andy Bernard and Karen Fillipelli (a potential love-interest for Jim).
However, besides the "loss" of Jim and Pam for the time being, the rest of the show still rolls along with laugh after laugh. Michael Scott shines brighter than ever, Dwight is still hilarious, and the supporting cast does a remarkable job of keeping themselves relevant to the ongoing storylines.
Thus, although this season is a bit weaker than the two previous ones due to the factors described above, I have to give the writers/creators credit for not falling into the trap of repetition and allowing the show to grow stale. Instead, they stretch things in a whole new capacity and, by the end of the season, end up a better show for it going forward.