I have no real favorites, some time ago it was one list of some missions, now it would be other.
Several years ago (circa 2017-2018):
Penny Dreadful (especially, 3)
House of Locked Secrets
Return to the City
Lich Queen's Demise
No Honor Among Thieves
Full Moon Fever
Now:
Painter's Wife
Hazard Pay
Volta and the Stone
Chronicles of Skulduggery 1-3
Perilous Refuge
Iris
New missions don't "destroy" previous, but time flies and they sometimes do something new, and can be more accessible, though I may return and replay older works, older favorites. Perhaps, it would be even more interesting to see what are the best missions for newcomers, both well-designed and accessible.