An Unearthly Child (Pilot & Episode 1)/The Daleks/The Edge of Destruction
Available in the U.S. as "The Beginning" box set. This is where it all started back in November 1963. This release has both the unaired pilot of the first episode and the final aired version. Hartnell's Doctor is much more sinister and quite verbally abusive on the unaired pilot than in the final version of the first episode. You'll probably only want to sit thru the remaining three parts of the premiere story once as the caveman dialogue gets very tiresome, but there are some great character moments from the four regulars (The Doctor, Susan, Ian & Barbara).
"The Daleks" may best be viewed as two stories - episodes 1-4 are about the exploration of the city of Skaro, the introduction of the Daleks and escaping their clutches, while episodes 5-7 focus on our heroes teaming up with the Thals to defeat the Daleks before they drop a neutron bomb on the planet.
"The Edge of Destruction" is a two-part character study set entirely in the TARDIS. A cross between a Pinter play and a Twilight Zone episode, The Doctor and his companions let their fears and distrust of each other lead them to certain destruction. The scenes where a possessed Susan is threatening her fellow companions with a pair of scissors is quite frightening, and Hartnell is perhaps at his most sinister - at one point threatening to throw Ian & Barbara off the ship in mid-flight. We also see our first evidence that the TARDIS is a living being and not just a machine.
The Tomb of the Cybermen
Previously presumed wiped by the BBC, this four-part story from season 5 was rediscovered in the early 1990's in Hong Kong. It's the earliest surviving story of both Patrick Troughton's Doctor and the Cybermen, and it's also the only surviving story featuring companion Victoria Waterfield, a Victorian-era girl who joined the TARDIS crew in the previous adventure. Yes, the sets look cheap, the acting from the guest cast is quite suspect, and some story elements are just a little bit racist, but as an artifact from a lost era of the program it is a fascinating watch. Matt Smith cited this as his favorite episode, and Troughton's portrayal of the role (along with the bow tie) helped inspire him when taking on the role.
The War Games
Yes, it's 10 episodes, but it never seems to drag as much as other multi-part episodes from the black & white era. Aliens kidnap soldiers from various wars in earth history and brainwash them to make them all think they're still fighting in order to form the ultimate army to take over the universe. The story has probably the largest guest cast of any Who story, the highlight being Phillip Madoc's chilling portrayal of the War Lord. We are also introduced to the Time Lords and find out why the Doctor is on the run from them. This is Troughton's last story, and his farewells to his companions Jamie & Zoe are truly heartbreaking.
Inferno
My favorite Jon Pertwee story, featuring the Doctor's first journey to a parallel universe, in this case a fascist Great Britain facing an ecological disaster caused by corporate/government greed and the need for cheap sources of energy under the earth's surface. And the Doctor must get back to our universe in order to advert the same disaster.
Terror of the Autons
A sequel to "Spearhead from Space", the Autons return to take over the earth with the assistance of a new character - The Master! Roger Delgado is still considered by many to be the best Master, and his scenes with Pertwee are always a joy to see (they were great friends in real life). This story also sees the introduction of Katy Manning as Jo Grant, a bumbling but lovable agent of UNIT. This story generated a lot of controversy with scenes of suffocation by bean bag chair, a killer troll doll, and a policemen being revealed as an blank-faced Auton at the end of episode 2.
The Daemons
Another UNIT story featuring the Master, considered by many to be the best story from the Pertwee era. The stone gargoyle, Bok, predates the Weeping Angels by about 35 years. The Master, posing as the village vicar, dabbles in the black arts to summon the demon Azal (in reality another alien). The Brigadeer delivers his most famous line in episode 5 - "Chap with wings there - five rounds rapid."
Day of the Daleks
I have to throw in at least one more Dalek story in here, and this was the best of their three appearances in the Pertwee era. The Daleks take over earth in the 22nd Century, and freedom-fighters from that era travel back to the 1970's to attempt to change history. The story is available in both original and special edition. I highly recommend watching the special edition as the pacing is better, the special effects and CGI shots mix well with the original footage, and the original Dalek voices, which were very poor, are now replaced by current Dalek voice actor Nick Briggs.
Carnival of Monsters
A humorous adventure written by Robert Holmes. The Doctor and Jo land on a ship bound for Burma in the 1920's yet, all is not what it seems. This story is also available via Netflix streaming.
The Time Warrior
A psudo-historical set in mid-evil England, featuring the debut of the Sontarans (in this case, a lone Sontaran named Linx) and of Sarah Jane Smith (Elisabeth Sladen), the plucky journalist who, at first, believe it's the Doctor who's the villain. Again written by Robert Holmes. The guest cast includes Jeremy Bulloch, who went on to wear the Boba Fett suit in "The Empire Strikes Back" and "Return of the Jedi".
Planet of the Spiders
Jon Pertwee's swansong. A six-episode story, the Doctor must battle the giant spiders from Metebetis 3 for possession of the "Great Crystal" (a fragment of which appeared in "Hide", an episode from the current season). The majority of episode two is one big vehicular chase featuring hovercrafts, gyrocopters and speedboats (Fast & Furious it is not). The Doctor must face his fear and risk losing his life in the final confrontation with "The Great One", and in the end sacrifices his third incarnation to save the day. Lis Sladen's tears during his final moments were genuine.
COMING UP...THE BEST OF TOM BAKER!!!