Depends upon how long I'll be "sitting"
If short duration...
In Gear w/ clutch in - the throwout bearing is being used/worn (OK but not great)
If long duration...
Out of gear w/ clutch out - you'll likely wear the synchro's of the first gear you engage.
(often, instead of pushing into first and wearing those synchros, I'll click into a different gear (3 or 4) to stop the clutch from spinning and then move to first [i'd guess the first gear synchros get the most use/abuse out of the bunch])
Hypoid previously posted:
"I don't recall ever hearing a reason for keeping the tranny in gear, while sitting at a stop."
From motorcycle days - one big reason for leaving it in gear is if you're the last vehicle (or even second or third to last) in a line of traffic. Should a vehicle behind NOT stop you can quickly whack the gas, dump the clutch and move forward/out/escape - I'd often keep an eye on the mirror in those situations (perhaps wheels to the side to escape). A quite rare issue, and one a bit more difficult on a wide vehicle (vs. a motorcycle that can readily fit between or beside an in-front vehicle).