Pyramid-shaped memento box, possibly a terrarium available here.
HENKE-JECT Syringe. Visible in Hounds of Baskerville on top of Sherlock’s printer. Maybe to refill their ink cartridges? Or is it a 7% solution?
Poker ash jar available here. (On set it doesn’t have the lid and appears in every episode including the pilot.) There are also dice, a chess set, a Sudoku cube, Cluedo, & lotto scratch-offs. Games of chance and skill.
Sherlock’s magnifying glasses called “La Jumelle Mars,” invented in 1897 by León Bloch who also invented a stealth camera he called “Le Sherlock Holmes” in 1912. It’s in most (all?) episodes.
Two’s Company Large Horn Magnifier available here. Also in most eps. Especially visible in The Great Game.