Another great use is to Repel an enemy right before an allied Naga Siren ults - that hero won't be affected by the Song, so you can go right-click him to death before the Song ends, at which point the resulting team fight is 5v4, and, of course, you still have the opportunity to initiate with a perfect Echo Slam, Black Hole, Ravage, or what have you.
TP out of team fights safely by casting Sprout on yourself and teleporting out.
Walkways and ramps? Most are the perfect size to be blocked by a well-placed sprout.
Sprout gives vision as well: Cast up hills for a limited view of what's to come. Gives flying vision!
Sprout towers to block some (depending on attack range) melee attacks while allowing the tower to continue attacking.
(Obvious) Sprout is usable treant fuel, so use while pushing towers.
Teleport can be canceled, so use its obvious animation to intimidate enemies off your team members or force an enemy to TP to defend.
(Another obvious one) Cast your ultimate on the opposite side of the map so that it hits the target enemy with more damage as it bounces.
The spot on yourself then immediately use a teleport scroll. In theory, the tp scroll takes you to the base and the X pops you back in the lane a second later.
Puck - Blink dagger is usable during phase shift.
Clockwork - Clock's ult hits in an AoE Similar to Sven's stun
Shadow Fiend - Shadow Fiend gains souls off denies
Axe - Axe can ult couriers!
Since dark pact has a 1.5-second delay, if timed right, it can be used to escape stuns.
An example is CK's stun, if you dark pact right before it hits you, even if it is a 4-second stun, you should break out of it in about a half a second.
Queen of pain's shadow strike is not dispelled by slark's purge. This makes QoP a very good lane counter to him, as well as denying him his ult regen for the duration of shadow strike.
Not hero specific but if you have lost stats due to a spell (like undying's decay) this is the best time to regen that stat. Eating a tango while under decay will net you more health than without decay, likewise, a clarity when losing int due to astral imprison will net you more mana.