Ice Storm (Wraith, Rank 3)
Freezing a boss, fast-pummeling him, then stabbing him when he's down (perhaps with a side of Fury) remains a bread-and-butter tactic all the way to the endgame. As useful (if not slightly more so) than the freezing Hammer of Ergion skill upgrade you'll get much later.
Bird of Prey (Ranged, Rank 3)
Slows time without spending focus. You do need to be falling, but given your natural climbing ability (which is total), you're seldom more than a few seconds away from a decent plummet.
Shadow Strike (Ranged, Rank 5)
This teleporting killstrike has a near endless list of tactical applications. Use to quickly claim a sniper's perch, bypass traps and fortifications, to cross chasms, catch up with a fleeing enemy, pick a gem-carrier and his gem out of a crowd, and just generally become an angel of death. Paired with Quiver of Souls, the non-lethal variant lets you keep the streak going forever, and as complement to Shadow Mount it makes things like time and distance concerns for other, lesser persons.
Treasure Hunter (Wraith, Rank 5)
Seems a bit quotidian, but soon you'll wonder how you ever played without it. Not only it useful early on, but its skill upgrades are among the most useful in the game- Discerning Eye and Prospecting making the most of the game's relatively meagre loot, and the Mind Breaker upgrade is a terrific help against enemy captains in the thick of battle, at least until you have Shadow Dominate.
Wraith Chain (Predator, Rank 4)
A quick, silent, way to take out whole groups at once. Particularly handy for groups that could never be stealthed individually (eg they're all in a circle looking at each other). Especially handy for story missions, where events tend to lead you through corridors of clumped hostiles. Also good for trying to gain access to an ithildin wall rune when it's surrounded by idling enemies.