There's something perhaps a bit perverse in some of the strongest episodes of new Who emerging from the series which (arguably) had the weakest companion. Freema Agyeman was ill-served by writing that couldn't let her be a companion in her own right, as opposed to the-one-in-Rose's-shadow, and consequently never felt entirely comfortable in the TARDIS.
Series 3 has real highs and certain lows - the introduction of Doctor-lite episodes (to ease the production schedules) produced the inventive wonder that was Blink (and further proved Steven Moffat's genius), the unashamed grab for the heartstrings was perfectly realised in the Human Nature / The Family of Blood double-header, and the re-introduction of one of the Doctor's most enduring foes was well-judged. That said, we also had the inevitable return of the Daleks who already feel like they're in danger of over-exposure.
The Family of Blood
The Shakespeare Code
The Sound of Drums
Last of the Time Lords
The Runaway Bride
The Lazarus Experiment
Smith and Jones
Daleks in Manhattan
Evolution of the Daleks
Top 5 guest spots
1 Dean Lennox Kelly's rugged and omnisexually flirtatious Shakespeare was hugely charismatic
2 Almost unbearably poignant, Jessica Hynes' Joan Redfern's love story with the human John Smith is magnificently done
3 A pre-Hollywood Carey Mulligan's Sally Sparrow - the best companion that never was
4 Tom Ellis all stubbly is always a treat
5 Derek Jacobi's Professor Yana - I still get chills thinking about the epic reveal at the end of Utopia
A tie between the Face of Boe's heroic demise in Gridlock and Chipo Chung's gently elegiac and courageous Chantho.
Most wasted guest actor
Bertie Carvel's three seconds as The Lazarus Experiment's Mysterious Man is egregious, as is most every choice for Miranda Raison's New Yoik flapper.
Most important thing that is never mentioned again
I think most things in this series made sense or had their time and place, even the paradoxes, after all it's just "a big ball of wibbly wobbly, timey-wimey....stuff".
Gay agenda rating
B - Shakespeare and the Doctor makes for the kind of fanfic that (some) people dream of.