Wooper I don't know about, but because I have a hard-on for undead demon insects, I'll help you with Team Shedinja as best as I can.
First thing: Give all your Shedinjas Lum Berries. Leftovers and HP-restoring Berries are worthless on a 1 HP Pokemon, and everything else of much merit doesn't help since most other Berries require you to take damage (which Shedinja can't) before they activate. So, status-healing Lum Berries all the way.
Now, on to the team...
First thing a Ninja needs to know is the art of stealth. So, here's an evasive moveset for Shedinja:
Sand Attack
Double Team
Confuse Ray
Grudge
This guy is all about dodging and enduring opposing attacks. His goal is wearing down the opponent's PP (and HP in Confuse Ray's case) as much as possible without having to resort to Grudge, which is there because it's Shedinja's signature move and could always come in handy anyway.
Second, a Ninja must know the art of decoy. Ergo, a decoy Shedinja:
Double Team
Swords Dance
Baton Pass
Agility/Silver Wind
Send this guy against a harmless Pokemon, and then beef up his attack (and evasiveness and speed against a potentially dangerous opponent) to max, then switch him out for a heavyweight.
Third, a Ninja must be strong. So, a Physical tank is in order...
Hyper Beam
Shadow Ball
Slash
Return/Hidden Power (Rock)
This guy's job is like that of the anime Shedinja: Mow down the enemy with Hyper Beam (or Shadow Ball if any Ghosts pop up) or, against a weaker enemy, Slash (You may have to breed for this one.) The last move I couldn't decide on, so I left it as a toss-up between Return (a less powerful Hyper Beam that doesn't need a recharge) and HP Rock (the remedy for the Flying Pokemon that are the bane of the rest of this team). Your choice.
Fourth, a Ninja must be clever, and versed in a wide array of fighting styles. That's where this guy comes in:
Shadow Ball
Silver Wind
Dig
Toxic
This Shedinja is the Swiss army knife of the team - his attacks can lay waste to 9 different types of Pokemon (including 4 of the 5 types Shedinja is weak against), and his Toxic can eat away at the remaining 8. Quite handy to have around, and a likely candidate for team captain.
Fifth, a Ninja must master the art of surprise. For that matter, here is a more 'fun' Shedinja:
Snore
Mimic
Toxic/Swagger
Grudge
Opponents with a fetish for moves like Hypnosis and Spore won't work on this guy, and most power attacks he can simply absorb and throw right back at the enemy! Those that he can't he can incapacitate with Toxic/Swagger (Again, I couldn't choose.), or if the opponent is immune or already afflicted, Grudge the bastard and leave him/her/it powerless.
And finally, a Ninja must know the value of teamwork - Ninjas often work alone, but they must stand together when the situation calls for it. So, I've recycled a few moves from the other 5 Ninjas and put them on this last one; this is IMO a 'standard' Shedinja moveset:
Shadow Ball
Silver Wind
Grudge
Hyper Beam
Shedinja's best feature is its attack power - its speed and defense are only decent, and its HP and special stats aren't even worth bothering with. So, this Shedinja is all about hitting hard and fast, STAB'ing its enemies into submission, and of course using Grudge when the situation arises. It's just what Shedinja do.
Now, this moveset is far from perfect; in fact, it's probably the one post in this whole topic you should probably avoid entirely, but I think it works. Emphasis on 'think.' I dunno, though... Try it yourself if you want. You'll probably be surprised with the results.