This is definitely best used as a lead, so that entry hazards don't become a big problem. It also works as a spin blocker, so that helps, too.
Dark Ninja
Shedinja @ Focus Sash
Wonder Guard
Adamant/Jolly
252 Speed, 252 Attack
-Shadow Sneak
-Shadow Claw
-X-Scissor
-Dig
Shadow Sneak for some priority. Shadow Claw and X-Scissor are fore main STAB. Dig because it takes care of Rock-types and if the opponent uses EQ, you're still safe.
Special Ninja
Shedinja @ Focus Sash
Wonder Guard
Timid/Modest
252 Speed, 252 Sp Attack
-Shadow Ball
-Hidden Power (Water)
-Silver Wind/Bug Buzz
-Giga Drain
Considering it's dismal Sp Attack stat, I don't know who or why someone would use this set. Shadow Ball is a great STAB. Silver Wind or Bug Buzz is really up to you. Silver Wind gets the chance to raise all of it's stats (though the only to useful ones are Speed and Sp Attack) while Bug Buzz has more power and a Special Defense drop chance. HP Water takes out two of it's weaknesses. Giga Drain just for coverage and it really gets no better Special moves.
Support Ninja
Shedinja @ Focus Sash
Wonder Guard
Jolly
252 Speed, 252 Attack
-X-Scissor/Shadow Claw
-Confuse Ray
-Will-O-Wisp/Toxic
-Grudge/Spite
X-Scissor and Shadow Claw are there so you're not Taunt bait. Which one you choose is up to you. Confuse Ray is great. Nothing more needs to be said about it. Will-O-Wisp can destroy Physical sweepers like Haxorus (which will destroy this little bug due to Mold Breaker anyways) or Tyrannitar (which will Sandstorm or Crunch you to death), while Toxic can get rid of Pokemon with considerable bulk, like Blissey and Slowking. Grudge and Spite both lower PP, albeit Grudge completely destroys the PP but only if it faints. Spite lowers the PP of the last move used by 4 right off the bat, so again, it's a matter of personal preference.
Ah, as partners go, and you're not using it as a lead, anything that can change the weather to something more desirable or spin away entry hazards or you're not using this is a lead will work just fine. Here are a couple of examples:
Politoed @ Lum Berry/Choice Specs
Drizzle
Timid/Modest
252 Speed, 252 Sp Attack, 4 Hp
-Psychic
-Focus Blast
-Ice Beam
-Surf
This set is basically just a standard. Changes weather away from Hail or Sandstorm to Rain. Not bad.
Tentacruel @ Wise Glasses
Clear Body/Liquid Ooze
Timid/Modest
252 Speed, 252 Sp Attack, 4 Hp
-Rapid Spin
-Toxic Spikes
-Surf
-Blizzard
I use this set in my Soul Silver and it works wonders. It can spin away hazards while setting them up. Surf and Blizzard are just two amazing moves on their own, so that's why they're there.
Just a question: Can Wonder Guard be Skill Swapped? Because that then opens up huge options for a team.