Ninja/Dark and Ninja/Storm are the two best Ninja combos I know of. I don't know how well a Ninja/Therm or /Pain would do. They keep the Ninjas alive, and let them do what they are best at; deal out lots of melee single target damage.
/Storm and /Dark are also very good with Necro/ as well. My Necro/Pain and Necro/Therm are lowish level but strong so far.
Arc #40529 : The Furies of the Earth
I feel nin/ really needs a AOE heal and heavy debuffs or buffs to last so the best option there is /dark , but sense you don't want to play another /dark . I would say necro/storm would be you're best bet . With the self healing and crazy tohit debuffs from the lich stacking with hurricane .
The nin/ end of things with storm would be nice but not as tough , (Wish they would buff nin/ def a little >_< ) the best bet for them with out playing over something you have done would go to nin/therm . forged-smoke flash-oni would be fun 
I mite have to give nin/FF go . power boost and FF will cap there def unless they changed power boost sense last time i looked . Hmm just did the math and add the def pet IO genin would hit 45.83 with out power boosting bubs , at level 50 that is .
(Edit i wouldn't go with nin/pain sense it's lacking real buff a small res buff with mostly heals and regen mix that with melee pets and your going to be spamming heals all day you will with therm as well but not as much .
lol almost 4 years and only 9 post O_o game is to fun to spend to much time here 
)
Well theres my take on things hope it helps
I have a nin/pain at lvl 36 right now. They're crazy, I mean uncontrollable, A.D.D with crack smoke on top. That being said, they're the most brutal for ST damage and will kick, depants, and swirlee an EB as long as they're squishyness doesn't get them killed, and if it does, the summon animation is very short, so resummoning on the fly is easy. (no typing on your wrist, using your walkee-talkee, etc.)
That's why I took /pain. the AoE and ST heals are great for them. Share pain is perfect for filling up a genins full hp bar, and World of pain is awesome for their hurtin' resistance. Once you get up to painbringer and anguishing cry it gets even better. I find the most survivability for the nin come from this combo. I'm sure others will debate that, but that's from my own experience.
Necro/Pain - Walking apocalypse of doom
Ninjas/Pain - Retarded "running" apocalypse of doom
Necro/Storm - Classic Banished Pantheon combo. Never fails.
Necro/Dark - AVs with AoEs will make you rage quit. Wonderful versatile combo
Ninjas/Thermal - Redonculous yet robust
Necro/Thermal - 2 words: Flaming Zombies
Thugs/Storm - Sho' 'nuff? Pretty decent for PvP and PvE
Mercs/Storm - Just crazy enough to work in most situations. Just set a timer while the Mercs attempt to kill things.
Quote:
With the Edict of the Master +Defense and Maneuvers, you'll break 45 on your positional defenses in the low thirties. It's pretty awesome (though the Genin won't be softcapped against most spawns, due to their -2 level).
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Originally Posted by Qwarg
I mite have to give nin/FF go . power boost and FF will cap there def unless they changed power boost sense last time i looked . Hmm just did the math and add the def pet IO genin would hit 45.83 with out power boosting bubs , at level 50 that is .
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No love for Ninja/Poison?
I have one at 39 and he's been a blast to play. Especially against the big single targets. Elite Bosses are a breeze to fight. Granted my ninjas do die alot, as I just started slotting alkaloid, but it's been a fun combo to play.
my ninja/poison is lvl 46 and will soon be my first lvl 50 villain. soloing EB's is cake.
FWIW, I am enjoying my necro/thermal. I don't mind when _one_ minion dies, because then I get extracted soul.
Triumphant Defenders Forever
Psylenz FF/Psi, ArticQuark Storm/Rad, Symon BarSisyphus Bots/psn, Max VanSydow Thugs/Dk, Cyclone Symon Bots/stm, Blue Loki Ice/Cd, Widow 46526
HelinCarnate:OMG it is so terrible. I have the option to take 3 more powers but no additional slots. Boo F'ing hoo.
Hey all.
After finishing off my last MM project, my thugs/traps, a month ago, I've been having the urge to come back to redside and roll up another MM. Now, I don't like to play the same power sets twice in an AT until I've exhausted the rest of them, so I know that I'd rather not roll another Bots/, Thugs/, Dark/, or Traps/. Mercs have never really appealed to me, but I'm willing to try them if there is a particularly good combo.
I was thinking about a necro/therm or /pain, but I've wanted to lvl up a ninja/ MM since I deleted my 25 Nin/FF a few years back. What do you all think? Is there a particular combo of Nin/ or Necro/ that does especially well? I want to have a *fairly* smooth ride up (mostly solo) without sacrificing too much end-game potential, it at all possible.
Thanks in advance!
~Alpha
"People are like stained-glass windows.
They sparkle and shine when the sun is out,
but when the darkness sets in their true beauty is revealed only if there is
light from within"