My favorite Sniper build:
Headshot
Squad Sight
Damn Good Ground
Battle Scanner
Opportunist
Low Profile
Either Colonel perk, they both rock, just in different circumstances.

Psi Powers:
Mind Fray
Psi Inspiration
Telekinetic Field

Armor: Ghost or Archangel
Weapon: Plasma Sniper Rifle
Item: S.C.O.P.E. (with Foundry upgrade)

Explanation:
Squad Sight is incredibly powerful, greatly extending the Sniper's range, keeping them out of harm's way.

Damn Good Ground is one I take for a few reasons. First, while it is a minor boost, it boosts The Sniper's main focus, rather than their off weapons. Second, once I get a Psi Sniper, I usually replace pistols with Mind Fray, which rocks.

Battle Scanner I pick up, only because Disabling Shot is relatively useless. Personally, I think making a weaker utility shot less accurate than a regular attack just kills it, especially since it buys you a turn, at most, and doesn't work on Berserkers, who, besides Sectopods, are the only enemy Snipers can't one-shot if they get a good crit.

Opportunist is awesome. Since a Colonel Sniper with a S.C.O.P.E. has better than 100 Aim, this makes their Overwatch shots (always taken against enemies out of cover, since they're moving) always hit, unless they have a dodge buff (fliers, mostly), and even then, at least 85% hit. Since it works with Squad Sight, this makes it a way to basically instantly kill or cripple a member of an alien squad that patrols into you. This FAR outweighs the 10% Aim boost on hurt targets, IMHO.

As for the Colonel perks, it depends on how you play. If you eliminate an enemy group's cover with explosives, In the Zone let's them finish everything off and still have time to move and reload. It is also absolute death to Chryssalids. And it does have some psynergy (synergy, dangit, too much Golden Sun) with Overwatch, as you will usually get an extra turn (3 moves) on the turn after you Overwatch kill something due to In The Zone refunding a move when it triggers. Slightly buggy, but useful. Double Tap is a better stand alone, more reliable ability that requires less setup, but is also less powerful.

Mind Fray is your first Psi power, and it rocks. On a Sniper with good Will, this should replace your pistol. 5 damage, plus a mobility, Aim, and Will penalty? Yes, please.

Psi Inspiration blows Psi Panic away. It buffs your Will, and removes Mindfray from your team while it's at it. Panic is unreliable, and can cause the enemy to get a free, high accuracy shot.

Telekinetic Field is a HUGE defensive buff. If your Sniper has nothing to do, you can put you entire team in the equivalent of High Cover, or Hunker Down those already in cover. This ability is AWESOME. Not as flashy as Mind Control, but, again, more reliable. It can save your butt in bad situations, doesn't require high Will, and doesn't have the negative impact of Mind Control. Plus, since Snipers are in the back, and Mind Control doesn't work with Squad Sight, Snipers are in the best position to drop a TK Field on your team without buffing the enemies too.

Archangel versus Ghost armor. Both are awesome. Archangel is more vulnerable, but you do get extra defense from Damn Good Ground, since you're flying. Ghost gives you fast movement, passive defense that stacks with cover, a grapple of limited utility that is great when you can use it, and four charges of a +100% Crit chance ability (bonus for cloaked units). Psi Armor is not horrible, but since Mind Fray is the only offensive Psi Ability my Snipers get, I tend to focus on other strengths.

Plasma Sniper Rifle is the best one in the game, obviously. Use it, love it.

The S.C.O.P.E. gives you +10 Aim and +10 Crit chance (once upgraded). Almost every other item is defensive or explosive, and Snipers are rarely in a position to use either. Go with the offensive buffs.