I rank the aliens of Doctor Who through 'classic', 'vintage', 'one-hit wonder' and 'others'.
CLASSIC MONSTERS/ENEMIES
Daleks
Cybermen
The Master
Weeping Angels
Classics are the pride and joy of Doctor Who. You can expect them to crop up on a rather regular basis, often in stories not limited to their own plots and schemes - they have a far wider scope within the series that can be explored. These are the ones that you're most likely to see on mugs, on t-shirts, in the playgrounds of schools across the UK and beyond. It's a very small list for me, as it takes a lot to reach a status like this. The Daleks, the Cybermen, the Master and the Weeping Angels are the only ones I'd put in this list, making the angels the only addition from NuWho so far. That's not a bad thing on NuWho's part - in eight series, it's impressive that a new creation has emerged that has such storyline longevity, is instantly recognisable and iconic and still retains an element of either mystery, fear or name-power.
VINTAGE MONSTERS/ENEMIES
Sontarans
Silurians
Sea Devils
Ice Warriors
Autons
Ood
Judoon
The Trickster
Vintages are the next rung down, and are the aliens that are likely to recur within the show but not necessarily very often. They're very much a part of Doctor Who's ongoing essence, but they might not be as recognisable by name to non-fans and don't quite have the simple grab-factor of more classic examples, such as the Daleks. From NuWho, the only real addition has been the Ood - a recognisable and distinguishable alien, though their story may well have been told already.
The Trickster from The Sarah Jane Adventures is arguably an indirect example of a 'vintage' enemy, appearing in three seperate stories (and a planned fourth from the aborted stories of Series 5) as well as warranting significant mentions in both Doctor Who: Series 4 and Torchwood: Series 4. Again, his story has likely already been told though he has encountered the Tenth Doctor already and there is room to bring back this sinister, iconic character.
The Judoon are possibly another, but have only had two stories (one in SJA) to prove their worth and haven't recurred barring 'kitchen-sink' moments.