Aerith and Bob: Gender-inverted: Sherlock and Beth (although it could be argued that their surnames, Holmes and Lestrade, play it straight).
Animal Motifs: Used sometimes in-universe. Holmes is described as alternately aquiline and feline (as per Canon), Ten's Puppy Eyes get mentioned a fair bit, Moriarty retains his serpentine qualities, and Moran is as much the tiger as ever.
Beauty Equals Goodness: We already know how good David Tennant looks, and Skyfire's illustrations with Holmes and Watson base the pair's looks off of Jeremy Brett and David Burke. Of course, Sally is a beautiful young woman, and Beth is pretty good-looking in the illustrations (which are a little different from her canonical look). Beth also teases Holmes by mentioning that Inspector Lestrade is not bad-looking, himself. Moriarty and Moran are never described in very great detail, other than both often wearing malicious expressions.
British Accents: Comes up every now and then. Holmes and Watson, of course, speak Received Pronunciation, which becomes important for Beth when she's working out who they are. Beth herself can speak a decent Cockney; her family spends summers in the UK, so she's gotten the hang of that particular accent without losing her own Midwestern one. The Doctor's own Estuary accent is mentioned early on in Holmes's thoughts. Kit deliberately switches from a Midwestern accent to a middle-class London one in 1940s New Mexico.
Broad Strokes: Most notably with the TARDIS, who is an active character in these stories.
Wham Episode: "Burn", wham. Holmes, rather than the Doctor, is possessed by the sun. "Child of Time", wham. A teenage Beth Lestrade from Sherlock Holmes In The Twenty Second Century makes her debut and makes the series a three-way crossover. "Watson and Sparrow", wham. Sally Sparrow is about to become the mysterious second Mrs. Watson. "Dynamics of a Point", wham. Holmes and Watson have a terrible break-up, Holmes is quite visibly darker, and Moriarty is Back from the Dead. "The Dying Detective", wham. Holmes manages to make himself just about as soulless as Moriarty ever was, and Beth is killed. ...it would almost be easier to give examples of episodes that don't deliver a wham.