I figure they had a fair shake already so I didn't include this one originally, but bringing in a classic Big Bad from the source always pulls in the punters. But what do we do different from last time we had Daleks?
One good trick is to have them acting significantly out of character...
I SAID EXTERMINATE!
Since these are monsters, having them appear friendly and helpful is a recurring trick - "WOULD YOU CARE FOR SOME TEEEEEA?" - but there are other ways to do it.
We've seen frightened Daleks, mad Cybermen, the Master gone berserk, Davros working undercover...
How about Sontaran peacekeepers working with a Sontaran diplomatic envoy? Silurians working with humans in a future colony? A Weeping Angel inspiring the legend of the Golem by protecting the people of the Prague Ghetto?
Of course, you'll need to consider why they're acting differently.
And being monsters, they'll often return to form at the worst possible moment. The emotional Cyberman Kroton turned his back on his people when they targeted the humans he'd befriended. The Master tried to use the power of the feral deathworld to his own ends. The Daleks have a history of treachery and deceit...
But equally, they might hold true. Dalek Sec argued for the value of humanity and died defending it, Dalek Caan saved reality from his own creator's plans. Kroton became a hero in his own right and a companion to the Eighth Doctor in the comics.
See also the non-Who-specific suggestions over here.
Example: Castle Of The Sontarans
Tracking the Alignment's magnosignature, the Doctor, Emily and Richard find themselves in a desolate world at the border of occupied space, held by Sontarans... determined to make sure that the Thing out in the darkness does not make it through to threaten the worlds beyond.
(I did this one already, but this seems like a good place to underline it.)
Bonus example: The Golden Idol
Hook: On a primitive, forgotten world, a cult attacks a tribe seeking prisoners for their god. And un-translated, the cult's battle cry is EX-TER-MIN-ATE!
Problem: A survivor of the destruction of the Daleks crashed here a year ago, its systems too damaged to move, to do more than snarl its demands at the inhabitants. Learning their language, it has used their belief that it is a golden idol sent by the gods to take over the tribe that found it, form a cult and start mining for the metals needed to repair its shell.
Complications: The travellers stumble across this as they're nearly knocked over by a tribe fleeing the cultists. A loose coalition of free people plan to strike at the mines and need all the help they can get.
Sub-Plots: The coalition includes escapees from the tribes that formed the cult, among others, and suspicions and old resentments linger under the surface.
Resolution: Agents of the Dalek in the Coalition camp capture one of the Companions to bring them to their idol, who demands that she touch him and renew him with the power of a time traveller, and TO BE CONTINUED!
Fun Stuff: Daleks! Dalek-worshippers! Anti-Dalek-worshippers!
Theme: Power corrupts. The most terrible thing can tempt the innocent.
Jungle of Terror
Hook: The travellers rescue the captured Companion before she can be forced to touch the Dalek's shell and they escape to echoing amplified screams of FIND THEM! FIND THEM! BRING THEM TO ME!
Problem: The Dalek now knows that there are time travellers here, and will stop at nothing to find them. It orders the cult to redouble their efforts to repair it, and to find the travellers and their TARDIS.
Complications: A Dalek cultist in the coalition camp stirs up trouble between two of the leading tribes while the travellers are away, and once they return they find one of the tribes leaving. Can the travellers turn them back?
Sub-Plots: With the Dalek pushing the cult to find the travellers, the slaves are poorly supervised. It would not take much to overthrow their remaining overseers and set them free.
Resolution: Stop the Dalek abusing this world. Destroy it, take it away, help it - stop it however you can.
Fun Stuff: Doctor Who And The Temple Of Doom!
Theme: But the tempted can refuse corruption and learn from what they turned down.