As with Seasons 29 & 30 of the Whoniverse I feel the multiple tv series that make up the Whoniverse work best in concert rather than as separate entities, with Season 31 having more obvious crossovers than previous seasons. I started making a list of how I felt the series was best viewed. This list changed throughout the run of the shows, but this list is what I ended up with.
Also as before I had some basic rules when creating this list:
Rule #1 was that the crossovers between the different shows had to be supported by the episode order. This meant that Season 2 & much of Season 3 of The Sarah Jane Adventures had to be included so that the 10th Doctor's appearance in Season 2 would make sense.
Rule #2 was similar to Rule #1, in that I decided that all multi-part stories should remain intact, uninterrupted; complete.
Rule #3 was to (wherever possible) place episodes together that support a cohesive continuity.
Sarah Jane appears in 20 episodes.
The Doctor appears in (including flashbacks / cameos) 11 episodes.
Captain Jack appears in 6 episodes.
Episodes are numbered per season in this section, not overall number.
Season 31: (2008-2010)
31x01 Day of the Clown, Part I
31x02 Day of the Clown, Part II
31x03 Secrets of the Stars, Part I
31x04 Secrets of the Stars, Part II
These 4 episodes of Sarah Jane placed after the Season 30 finale in which all of the Doctor's Companions abandon him help give the audience a sense of loss such as the Doctor is feeling. He's traveling all on his own, and likewise, because of that lack of companionship, we as the audience are not traveling with him. "Secrets of the Stars" however has several visual and auditory references to The Doctor & future ties to Torchwood as well.
In Part I of "Secrets of the Stars" the Doctor is referenced and the 10th Doctor is seen in flashbacks to "School Reunion" & "Journey's End". Also in Part I Sarah Jane mentions that Martin Trueman is using a Bio Damper; the Doctor used such a device in "The Runaway Bride". Also in Part I, the Draconians are mentioned; they featured in "Frontier in Space". In Part II a male French News Reader appears; this same character appeared in the Doctor Who episode "Army of Ghosts" & later appears in Torchwood's "Children of Earth". In Part II news reporter Trinity Wells appears; this same character has appeared in several Doctor Who / SJA episodes & later appears in Torchwood's "Children of Earth". Sarah Jane mentions she knows "what it's like to be taken over"; she'd previously been possessed in "Planet of the Spiders", "The Masque of Mandragora" & "The Hand of Fear".
31x05 The Next Doctor
As mentioned before, the Doctor is traveling on his own and his sense of isolation is reflected in the audience who only gets to see isolated adventures of his; this being the first.
Thanks to events in the previous season finale the Cybermen are allowed to return. Doctors 1-10 are seen in a Cybermen info-stamp. The events of this installment will later be referenced in "Flesh and Stone".
31x06 Mark of the Berserker, Part I (Daleks, Slitheen & Sontarans mentioned)
31x07 Mark of the Berserker, Part II
31x08 The Temptation of Sarah Jane Smith, Part I (The Doctor / TARDIS mentioned)
31x09 The Temptation of Sarah Jane Smith, Part II (The Doctor / TARDIS referenced)
31x10 Music of the Spheres
A Doctor Who special mini-episode, this one features a Graske pestering the Doctor. It's possible that this Graske is the same one released at the end of the previous installment of The Sarah Jane Adventures, giving the feeling that the two shows are now playing off each other, especially after the references to The Doctor & the TARDIS in the previous 2 installments.
31x11 From Raxacoricofallapatorius with Love (K-9 Mark IV, The Slitheen)
This episode is usually considered to take place after 'Enemy of the Bane' (which aired before it), but I thought having two mini-episodes play off one another worked better, so when Music of the Spheres was set as 31x10, this installment followed as 31x11. It continues the feeling that Doctor Who & Sarah Jane are playing off each other.
31x12 Enemy of the Bane, Part I (The Brig)
31x13 Enemy of the Bane, Part II (The Brig)
A sequel to 2 Season 30 stories ("Invasion of the Bane" & "The Last Sontaran") this story also features UNIT which plays a part in the next installment ("Planet of the Dead"). This episode is the first appearance this season of a Sontaran. We will see other Sontarans later in the season.
These episodes also feature 3 returning Whovian guest stars: Mrs. Wormwood from last season's Sarah Jane Adventures episode "Invasion of the Bane". Commander Kaagh from last season's Sarah Jane Adventures episode "The Last Sontaran". And more impressively, Brigadier Sir Alistair Gordon Lethbridge-Stewart, who on Doctor Who was a companion to the 2nd, 3rd, 4th, 5th & 7th Doctors (having last appeared in Season 26's "Battlefield"). His portrait has also been on display in Sarah Jane's attic.
31x14 Planet of the Dead ***
This adventure is referenced in the next installment, and features UNIT, which was featured in the previous story.
"But you be careful because your song is ending sir." - Carmen
"What do you mean?" - The Doctor
"It is returning...it is returning through the dark. And then Doctor, oh but then...he will knock four times." - Carmen
This prophecy spoken by Carmen (a low-level psychic) recalls the Ood prophecy from "Planet of the Ood", and refers to events that unfold in "The End of Time, Part II".
31x15 Mona Lisa's Revenge, Part I **
31x16 Mona Lisa's Revenge, Part II **
Even though these episodes aired later in the season and feature K-9, the version that appears here is NOT the version from the rest of the series and can thusly take place earlier in the season.
There is a reference to K-9 being out of bounds to Luke but there's nothing saying that K-9 is living with them (as he does later in the season) and it's been demonstrated in several episodes that K-9 can leave his Black Hole Project; most recently in 31x11. He also left in Season 30 installments "The Lost Boy, Part II" & "Journey's End".
The Bane, last seen in "Enemy of the Bane" are referenced twice in Part I; The Sontarans are also referenced; both were seen only 2 installments ago, giving more weight to the references here.
One of the plot elements of "Planet of the Dead" involves Lady Christina de Souza stealing the Cup of Athelstan from a London museum on Easter. In Part I of this story, Lionel Harding refers to that event when he says: "I told them security had to be improved here. I told them. After that Cup of Athelstan fiasco at Easter." Having this installment air directly after 'Planet of the Dead' continues the feeling that the 2 shows are interconnected.
31x17 Prisoner of the Judoon, Part I
31x18 Prisoner of the Judoon, Part II
Sarah Jane has been possessed before in "Planet of the Spiders", "The Masque of Mandragora" & "The Hand of Fear". The Shadow Proclamation is referenced in Part I; they were last seen in #804 "The Stolen Earth". The Judoon appear in Parts I & II; they've been mentioned on Sarah Jane before but until now have only appeared in Doctor Who episodes (#741 Smith and Jones, #803 Turn Left, #804 The Stolen Earth). They will appear later in the season as well. "Dreamland" is referenced by name, and the spacecraft the nano-forms create for Androvax in Part II is said to be based on the design of the crashed Roswell spaceship; indeed the look of the ship (and it's power source) is identical to the visuals of said craft in the following Doctor Who story - a nice crossover ;-0)
31x19 Dreamland
Dreamland was easily placed here as this special animated installment of who is referenced verbally and visually in the previous Sarah Jane Adventures installment. Other imagery from this episode is rumored to appear in later Sarah Jane episodes.
31x20 The Mad Woman in the Attic, Part I ****
31x21 The Mad Woman in the Attic, Part II *****
The Time War is referenced in Part I. Maria Jackson is seen in flashbacks to "Whatever Happened To Sarah Jane?" & "The Last Sontaran, Part II". Luke's past timeline features scenes from "Invasion of the Bane" & Maria telling him about her moving in "The Last Sontaran, Part II". Sarah Jane's past timeline features scenes from "The Temptation of Sarah Jane Smith", "Day of the Clown", "Whatever Happened to Sarah Jane?", "The Time Warrior", "Planet of the Spiders", "The Hand of Fear", "The Five Doctors" & "The Stolen Earth". K9 Mark III appears in flashbacks in Part II (from "The Five Doctors"). The 3rd Doctor appears in flashbacks in Part II (from "The Time Warrior" & "Planet of the Spiders"). The 4th Doctor appears in flashbacks in Part II (the farewell scene between Sarah Jane & the Doctor from "The Hand of Fear" - which will be echoed in "The Wedding of Sarah Jane Smith, Part II"). The 10th Doctor appears in a flash-forward in Part II (to "The Wedding of Sarah Jane Smith, Part II"). In Part II, K9 Mark IV's mission from "Invasion of the Bane" finally comes to an end and he's able to return to Sarah Jane permanently. Sections of this story are set in the year 2059, which is the same setting as the upcoming Doctor Who story "The Waters of Mars". The Daleks appear in a flashback to "The Stolen Earth"; a Dalek from that story also features in "The Waters of Mars".
31x22 The Wedding of Sarah Jane Smith, Part I *****
31x23 The Wedding of Sarah Jane Smith, Part II ****
The Travist Polong alien from "Mark of the Berserker, Part II" returns in Part I of this adventure. The Trickster, last seen in "The Temptation of Sarah Jane Smith, Part II" returns here. The 10th Doctor appears in both parts of this story, as does K-9 Mark IV.
"Who are you, a man who has lost everybody, to talk to me of loneliness when The Gate is waiting for you?" - The Trickster to the 10th Doctor - a reference to the fast approaching "The End of Time".
31x24 The Waters of Mars ****
The prophecy from "Planet of the Dead" is referenced here.
The events of this installment are referenced in "The End of Time, Part I".
31x25 Children of Earth: Day One ****
31x26 Children of Earth: Day Two ***
31x27 Children of Earth: Day Three ****
31x28 Children of Earth: Day Four *****
31x29 Children of Earth: Day Five *****
Torchwood pops up again 25 episodes after last being seen in Doctor Who's "Journey's End". The long gap helps explain the absence of Martha Jones & Mickey Smith who seemed likely to join at the close of their last adventure - while 'Day One' lets us know that Martha is on her honeymoon. UNIT has a strong presence throughout each of the five installments, after last being mentioned in "Prisoner of the Judoon". Col. Mace (last seen in "The Poison Sky") is referenced in 'Day One'. The Doctor himself is mentioned in 'Day Three' & 'Day Five'. The first mention ties directly into the events of the Doctor Who episode "Utopia", while the latter reference ties more into the themes explored in "The Fires of Pompeii" & previous installment "The Waters of Mars". Also, the ending of 'Day Five' sets up Jack's appearance in "The End of Time, Part II", while the events of these episodes are referenced in "The End of Time, Part I". The reference to Martha Jones on her Honeymoon in 'Day One' are paid off in "The End of Time, Part II" as we see her and her husband. It also seemed important to have a story between "The Waters of Mars" & "The End of Time, Part I", as it's clear at the start of the latter, that the 10th Doctor has had several adventures since the closing moments of the former. Trinity Wells, who appears in 'Day Three' & 'Day Four' has previously appeared in Doctor Who episodes ("Aliens of London", "World War Three", "The Christmas Invasion", "The Sound of Drums", "The Poison Sky", "Turn Left" & "The Stolen Earth") and Sarah Jane Adventures episodes ("Revenge of the Slitheen, Part II", "Secrets of the Stars, Part II"); she returns to Doctor Who in the next 2 installments ("The End of Time, Part I" & "The End of Time, Part II" - creating a consecutive crossover appearance! Also, the male French News Reader has also appeared in Doctor Who ("Army of Ghosts") & The Sarah Jane Adventures ("Secrets of the Stars, Part II").
31x30 The End of Time, Part I ****
31x31 The End of Time, Part II ****