Season 1  (2002-2003)
(13 Episodes In Season 1)

Mr. Monk And The Candidate (In progress)
Mr. Monk And The Psychic
Mr. Monk Meets Dale The Whale
Mr. Monk Goes To The Carnival
Mr. Monk Goes To The Asylum
Mr. Monk And The Billionaire Mugger
Mr. Monk And The Other Woman (In progress)
Mr. Monk And The Marathon Man
Mr. Monk Takes A Vacation (In progress)
Mr. Monk And The Earthquake
Mr. Monk And The Red-Headed Stranger
Mr. Monk and the Airplane

Season 2 (2003-2004)
(16 Episodes in Season 2 - next half in January 2004)

Mr. Monk Goes Back To School
Mr. Monk Goes To Mexico
Mr. Monk Goes To The Ballgame
Mr. Monk Goes To The Circus
Mr. Monk and The Very, Very Old Man (In progress)
Mr. Monk Goes To The Theatre (In progress)
Mr. Monk and The Sleeping Suspect
Mr. Monk Meets The Playboy (In progress)
Mr. Monk and The 12th Man

There is also an excellent archive of transcripts on the following site
The Desk of Adrian Monk