Template 6: Major Alien Crisis
The name says it all; aliens (or unearthly creatures) have decided to conquer, destroy, enslave or recycle Planet Earth, usually causing panic on a worldwide level, with lots of alarming TV broadcasts, government communiqués, emergency meetings, armed forces running around and, of course, UNIT intervention.
Because of the scale of events involved, episodes which follow this pattern are almost always two-parters, like The Aliens of London / World War Three, Rise of the Cybermen / The Age of Steel, Army of Ghosts / Doomsday, The Sontaran Stratagem / The Poison Sky or The Stolen Earth / The Journey's End... but this template can also be found in some Christmas specials, such as The Christmas Invasion or The Next Doctor.
Combining this template with the previous one (Lives Less Ordinary) gives us what we might call the "smalltown invasion variant", in which the perception of the alien menace has not reached the authorities or the medias and is limited to a small community, either because some secret plan is only beginning to unfold (The Hungry Earth / Cold Blood) or because the goals of the aliens is more limited or specific in scope (Human Nature / A Family of Blood) - but the pattern remains the same: all these stories deal with the ways human beings deal with menaces which threaten their world, whether "world" here means planet, family or village. In all cases, enemies must be fought and tough choices (including some sacrifices) must be made.
Template 7: Timey-Wimey Stuff
These episodes deal with the more complex, subtler or chaotic aspects of the Doctor Who reality - time loops, paradoxes and other weird temporal phenomena. In these stories, the Doctor and his companion(s) must face the sometimes very dangerous consequences of travelling through time and tampering with history - whether this tampering is caused by their own decisions (such as in Father's Day) or by someone or something else's actions (such as In The Girl in the Fireplace, Doomsday, The Sound of Drums / Last of the Timelord or Turn Left). In most cases, the solution of the problem comes from the same source as the problem itself, the possibilities and implications of time travel and temporal manipulation (as demonstrated by Blink and its wonderfully non-chronological storyline).
This template can also be extended to stories in which reality is warped or manipulated, such as in Amy's Choice; it works equally well on a personal, almost intimate level (Amy's Choice, The Girl in the Fireplace), in which case it is often combined with template 8 (Crossroads, see below) or on a grand, universe-shattering scale (The Sound of Drums / Last of the Timelord or The Pandorica Opens / The Big Bang), in which case it is often combined with the Big Season Finale template (see below too); both extremes can also be combined, such as in Turn Left, in which the apparently trivial decisions of a single individual actually affects the whole of reality.
Template 8: Crossroads
This template, which could also have been called "dilemmas", deals with crucial, life-affecting choices which must be made by one of the Doctor's companions or, perhaps more rarely, by the Doctor himself - and with the often painful consequences of such decisions. It is probably the more personal and intimate template, since it deals directly with a major character's conscience, morality or feelings and often involves a touch of tragedy. Ultimately, all these stories deal with the theme of Destiny. It should be noted that this template is often combined with the previous one, Timey-Wimey Stuff (Father's Day, The Girl in the Fireplace, Turn Left or Amy's Choice); it is also present in The Waters of Mars, in which the Doctor makes the decision of altering a fixed point in history and must deal with the consequences of this choice (the fabulous "Time Lord victorious" bit). It can also be found in Big Season Finales, especially those in which a companion leaves the story (as Rose in Doomsday) or in which the Doctor regenerates.
Template 9: Who is the Doctor?
This template corresponds to what many DW fans call "Doctor-lite episodes", such as Love & Monsters and Blink, i.e. stories in which the Doctor merely lurks or runs around in the background while another character (such as Sally Sparrow in Blink) occupies the front stage; such episodes tell the story of someone's encounter with the Doctor - but from that person's point of view. In RPG jargon, these are episodes in which the Doctor and his companion are treated as NPCs - which makes this template a bit difficult to use in a campaign with Time Lord (or, at least, time travelling) player-characters... but makes it particularly interesting for one-off scenarios which use "normal people" as their main protagonists; it is definitely the template to use if you want your players to discover during play that they were actually playing Doctor Who all along.
This template is also present (without being prevalent) in The Lodger, in which the Doctor does play the "mysterious visitor" part, but which cannot really be labelled as a Doctor-lite episode. Because they deal with ordinary people facing extraordinary events, such episodes often combine this template with the Lives Less Ordinary or Crossroads templates.
Template 10: Big Season Finale
This template is always used for the epic two-parters which conclude each season of the show: Bad Wolf / The Parting of the Ways, Army of Ghosts / Doomsday, The Sound of Time / Last of the Timelord, The Stolen Earth / The Journey's End or The Pandorica Opens / The Big Bang. More than a scenario template in its own right, it combines the elements of several templates (such as a Major Alien Crisis, Timey-Wimey Stuff or Crossroads) into a grand-scale, spectacular, climactic confrontation. In most cases, this combination is made even more powerful by what we might call the "Nemesis element" - the opponent(s) the Doctor must face in such episodes are almost always old enemies of his, such as the Daleks, the Cybermen or the Master, arch-enemies which go back to the days of the Classic series and whose destinies seem to be cosmically tied to that of the Doctor himself; we also see this logic at work in the two-part special The End of Time (a "season finale" of sort), in which the Master AND Rassilon return (you probably don't get more "major" than this as far as Time Lords are concerned) to bring the Doctor's Tenth Incarnation to a tragic, beautiful end.