A step down from the Big Four, some monsters have returned often enough to have their own recurring tropes and foibles. They might never get a series finale but they'd get an opening episode or a mid-run two-parter and a couple of action figures...
"At the Sontaran Military Academy we have hatchings of a million cadets at each muster parade."
With a bit of name recognition before their return in the new series (and The Sarah Jane Adventures as well) the Sontarans have been around a bit. Lacking the faceless simplicity of Daleks or Cybermen and relying more on casting and prosthetic effects, they were never consistent until the new series despite supposedly being a near-identical clone race. But the game doesn't have to worry about 70s TV effects budgets, so feel free to have them arrive in their hundreds all the same height and build.
Quite erudite on their chosen specialist subject (WAR!) and willing to be practical and dishonourable but resentful when called on it, they tend to be militaristic jerks, sneeringly superior while happy to cheat, but quite advanced in a number of ways, and individual Sontarans can fit various war (WAR!) story character archetypes like the cynical veteran and the idealistic private. They also love using other species' scientists to work for them.
Sontaran adventures will generally feature war (WAR!), weapons, scientific advances, the ethics of cloning and the like. Sontarans can also make solo guest appearances if you need a warrior or military type (WAR!) or an "are we so different really?" alien if the travellers get captured by an outside force or something of the sort.
A spherical alien vessel descends on a small town near an Air Force Base. People in the facility start to go missing, or to behave out of character. Are the Sontarans manipulating them... or are they hunting the shapeshifting Rutans?
Silurians and Sea Devils
The Silurians mostly appear to be used for "are we so different really?" stories about various tribes fighting over territory. Despite the archetypal Bug Eyed Monster look straight out of the Black Lagoon they could occasionally evoke some sympathy as ousted former masters of the world. Plus, dinosaurs.
The surprisingly un-Lovecraftian Sea Devils (actually rather cute thanks to their turtle faces) first appeared as dupes for the Master, then as rank and file for their cousins. Nowadays the Silurians are back but they've borrowed some of the Sea Devils' dress sense, their disc guns and their string vests.
So, ethnic clashes, a bit of environmental concern, and rising from the depths to attack oilrigs.
What is that scaly green face doing in the crowd in a painting of one of Henry the Eighth's marriages?
More lizards and warriors, although despite the name (not their own choice, one they've been stuck with since meeting humans in their first story) they're less focused on war (WAR!) than the Sontarans. Their various appearances have made them a classic Proud Warrior Race with good and bad members, so they can easily be straightforward berserkers or reasonable ambassadors, sometimes in the same group.
Useful for rough-and-ready alien invaders, BEM stories or as representatives of a more unified future. Basically the same job as the Klingons in the various Star Trek series without the bashful charm.
A Mars rover goes offline shortly after seeing what looks like a big green foot. Are the Ice Warriors back, and if so, why now?
The Autons (and equivalent androids like Roboforms, Yeti, Slabs, and indeed Androids) are obviously good for not-as-they-seem stories, and the Autons in particular for commentary on consumer culture and the obvious creepiness of mannequins. They come equipped with varying speed and clumsiness levels as required to be scary or effective.. They can have human-seeming spokesmodels for dialogue, or swirly octopus things for a more direct meeting with the boss.
On the whole they're not story starters, more props for a villain, although it's possible to focus a story on their oddities. In general, they're a (somewhat) subtle alien invasion story tool. That said...
It's the twenty-fourth century, and Autons are everywhere... because the Nestene are selling them as must-have accessories, your own personal unthinkingly loyal plastic servant. Blank-faced bodyguards are the in thing for celebrities looking to demonstrate their wealth. The possibilities are obvious, but what are the Nestene getting out of the deal?
After two stories in the Ninth Doctor's run the Slitheen became the Big Bads of The Sarah Jane Adventures where their farting has less drama to damage, although their tendency to kill, eat and skin their victims has been sidelined a bit.
Raxacoricofallapatorians aren't all Slitheen, which means non-crooked examples could turn up (and almost did in The Stolen Earth but the scene was cut) so they could make for interesting juxtapositions, while the Slitheen lend themselves to crime stories scaled up to planetary levels.
A gang of several species lead by a Slitheen couple plan to steal Voga, the Planet of Gold! How would that affect the Cyberwars, let alone the galactic economy?
"Scopo trono frojo kofo todo!"
A new monster that can stand alongside the classics, literally in the front row of the Pandorica Alliance. The Weeping Angels could go the distance as well, but they've only been written by one person so far and they don't have a funny voice to imitate.
Lawful Stupid jobsworth security guards also used as boot boys by the Shadow Proclamation, individual Judoon might be smarter than that and willing to stop disintegrating people long enough to work with Whoniverse heroes (or villains if the need is great enough) to save the day.
So they're ideal "obstruction" monsters rather than real villains - they're still lethal but they can be talked down as well as outrun. If a spaceship has a plodding by-the-book policeman, he could easily look like a rhinoceros.
A blockade of Judoon ships covers a planet the travellers have to get to - can they persuade or evade their way past them?