Did the show always have this sort of humor running throught each episode which i just find annoying
If you are referring to the Classic era then no it didn't, something that lasted 26 years obviously had more than it's fair share of crappy humor but there was also some genuinely funny stuff.
Anything written by Robert Holmes usually had some understated but brilliant satirical humor and some of the best comic double acts in the show's history came from him as well including Jago & Litefoot in "The Talons of Weng-Chiang" and Garron & Unstoffe in "The Ribos Operation".
The 2 stories written by Douglas Adams also had some great moments and "City of Death" in particular has what I consider the funniest scene in Who history ( where the Doctor meets the Countess ) and a brillliantly hapless detective who tries to solve everything by punching/breaking things which draws some great remarks from both the Doctor & Romana II.