This build offers Skarner users a balance of damage, tankiness, and utility for laning purposes only. I've not tried jungling with Skarner just yet, so I don't know if this would work for jungling. Feel free to try it out if you want, but my recommendation is to use this build for laning only.

Greater Mark of Magic Penetration - Makes all of Skarner's damage skills hit harder.
Greater Seal of Scaling Mana Regeneration - Helps Skarner stay in lane longer, and be independent of the blue buff by mid to late game.
Greater Glyph of Scaling Mana Regeneration - Same reason as Seals. Skarner invested 21 in Defense to stay alive, so he'll need mana regen utility in order to stay in the laning phase.
Greater Quintessence of Ability Power - Early Game damage. This helps Skarner clear creep waves and harass better during early game. It also helps him heal up a tad better.

Offense: 9 - Standard caster configuration. Needs the 15% Magic Pen. to deal good damage with his skills.

Defense: 21 - Skarner needs to be able to get within melee range without dropping like a fly in order to be effective. Runes are supplying Skarner with "utility" so as to be balanced.

Utility: 0 - Runes cover the utility Skarner needs to be balanced.

Mercury's Treads - The game's loaded with "crowd-controlling" champions that stun, fear, silence, slow, etc.. It also reduces AP caster damage a good bit.
Wriggle's Lantern - Great sustain, minion-proc'ing to farm lanes and jungle, and armor vs minions and AD carries.
Trinity Force - Absolutely the best, and "key" item for Skarner. Proc, snare, health, mana, and move and attack speed all benefit Skarner greatly.
Hextech Gunblade - Maximum sustain, amazing damage, and nifty Active snare.

Doing well?
AP Damage Route:
Void Staff - All good players always build magic resist, and Void staff is the counter for it.
Rabadon's Deathcap - The best damage AP item money can buy, hands down.

Need added Defense?
Tank Route:
Guardian Angel - Two-in-One armor/magic resist compression, and you get a chance to escape after your health reaches zero.
Banshee's Veil - Spell block, more health, more mana, and more magic resist since Guardian Angel has low MR on it.

Crystal Slash (Q) - aoe damage (around you)/slow; use this to chase enemy champs, or slow them down to prevent deaths.
Crystalline Exoskeleton (W) - Chase/Escape skill with attack speed, movement speed, and a shield.
Fracture (E) - AoE damage spell (linear/in a straight line); kill creep waves, and blast clunked up enemy champs.
Impale (R) - Grabs enemy champ for 1.5 seconds; use this to pick out the enemy carry or squishy from the back lines and pull him back towards your allies for focus-firing.

I typically chase with Crystalline Exoskeleton(W), then Crystal Slash (Q) and Fracture (E), then suppression-grab with Impale(R) and pull towards my allies, then Crystal Slash (Q) and Fracture(E). Rinse/Repeat.

Ignite - Prevents annoying sustain champions from healing up during ganking and take-downs. without it, you may lose fights.
Flash - Get out of jail free card. Use this to escape whenever necessary, or to flash in and suppression-grab with your (R).

Other Summoner Spells?
Ghost - Decent and versatile. Though Skarner already has his Crystalline Exoskeleton (W) for movement speed, if the shield is depleted, the effects are gone. Ghost can help you escape better because it doesn't go away like Crystalline Exoskeleton (W) does.

Exhaust - It's good for coordinated games[aka: Arranged Teams]. You can exhaust an enemy champ and rake in a kill pretty easily with it, but for Solo Queue it's not that great imho.

Cleanse - Pretty good spell. You can use it to force your way into team fights, or forcefully escape away from being ganked.

Clarity - Though it helps with mana, in serious games [aka: Ranked/Arranged] it's more than likely looked down upon as sub-par. You can take this in Coop. vs. AI and maybe even normal unranked games, but for serious ranked play, you should stay away from Clarity.

Teleport - Good for normal and coordinated games. You can set up for quick turret take-downs with this spell. The only problem is that you don't have the reductions from the Utility line, nor do you have a point in it. It's possible invest into teleport with Skarner, but I recommend using Utility and armor/mr flat runes instead to maximize on this. Otherwise, I'd say stay away from teleport if you can.

Clairvoyance - Decent skill. You can spot enemies that get away with low health and use that to your advantage. Only problem is you don't have 21 Utility to reduce cool-down and increase its duration. It's best to reconfigure your runes and masteries to accomodate using it, otherwise I'd recommend not using it.

Smite - Best jungling spell for junglers. I don't recommend this spell with my guide. It's a better idea that you find a jungle guide to Skarner instead. You can try it, but I can make no guarantees as I haven't jungled with Skarner just yet.

All other summoner spells that I have not mentioned are sub-par [Fortify, Heal, Revive, Rally].

PROS:
Good AoE damage.
Great Durability.
Great Sustain.

CONS:
Isn't full-blown Carry.
Isn't full-blown Tank.
Ignite can really screw him over.

OVER-ALL:
Balanced and fun to play as Skarner.

You'll be pretty beefy and effective with this guide, and be able to take down them squishies. This is not an AP carry guide, but rather an AP Tanky/DPS variant. Good luck, have fun, and enjoy!