Hmm...
Here is what I've found to be nice pairings (In no particular order):
Ninja/Dark
Thugs/Traps
Bots/Traps
Necro/Dark
Merc/Storm
Demon/Therm
As you can tell, I like /Dark and /Traps... 
If I was going to pair them off without any repeats I'd probably say:
Ninja/Dark
Thugs/Pain
Bots/Traps
Necro/Poison (If you can handle the single target nature)
Merc/Storm
Demon/Therm
Let's see... If I was going to make one of each MM primary without duplicating secondaries I'd probably go with:
Bots/Traps (the ultimate soloist)
Demons/Thermal (resist based pets + resist shields = pets that can actually take hits)
Necro/Dark (very thematic, and insane amounts of control)
Thugs/Pain (no particular reason other than both being good solid sets)
Ninjas/Storm (Hurricane might actually keep the stupid Genin alive)
Mercs/Trick Arrow (because I don't like /Poison and /FF is too boring)
Ninjas/FF is also good if you just want to keep the ninjas alive, but the lack of debuffs or heals makes /FF a very boring set to play.
Cascade, level 50 Blaster (NRG/NRG since before it was cool)
Mechmeister, level 50 Bots / Traps MM
FAR too many non-50 alts to name
[u]Arcs[u]
The Scavenger Hunt: 187076
The Instant Lair Delivery Service: 206636
It's not an easy backstory, but I love Bots/Storm. Ranged knockback blasters don't mind the storm effects at all. It works together so well.
If you can't get your head around that Bots/Traps is a beast, too. This is uber all around.
Thugs/poison is an iconic pairing. The thugs keep each other alive fairly well except for the suicidal pyromaniac. Noxious gas was made for a Bruiser.
Ninja/Forcefields is another stretch, but the stacking defense is useful. Bubbles protect the kamikaze ninjas about as well as anything.
Necro/Dark is a fantastic pairing. The smaller zombies fit well within shadow fall and twilight grasp. This pair has its own vibe, but its extremely sturdy.
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.
Demon/Dark is a powerful combo.
My guides:Dark Melee/Dark Armor/Soul Mastery, Illusion Control/Kinetics/Primal Forces Mastery, Electric Armor
"Dark Armor is a complete waste as a tanking set."
Not as many responses as the brute thread but so far, necro/dark and bots/traps, demon/thermal and thugs/pain are obvious winners. Thanks guys.
I will remain a soldier until the war is won.
Going on the "No repeats" rule and based first on what I've tried and then what is left and sounds like fun / useful
- Necro/Dark : My original Villain and one of my fav characters.
- Thugs/Traps : Another combo I have. Good fun
- Demons/Pain : Just trying this combo now as a soloist. It may annoy me too much once I get the screeching demons at 12/24 of course.
- Mercs/Storm : 6 Ranged Henchies + Hurricane? Yes please
- Bots/FF : I've no real intention of playing either. Bots annoy me. Thematic combo though
- Ninjas/Thermal : Changed my vote to this simply because Thermal is more likely to keep the Ninjas alive.
Bots/traps Just such a tasty combo
Thugs/dark Having a lot of fun with this one
Merc/Storm Also fun. The chaos of storm goes well with the order of the mercs
Demon/Thermo Just a good thematic pair, and stacking resist on resist is never a bad thing
Necro/Pain Would be very hard to die, but may be a bit slow in killing
Ninja/Poison Another good theme.
Hmm...
*runs off to make more masterminds*
Bots/Dark - Only MM I've made on live servers and is just a damage sponge. When the pets behave its so much fun, when they don't I ignore playing him. This was also my 1st toon when I started playing back in Dec 2005. He's usually my purp/inf farmer and GM hunter, oh and badger.
Demons/Therm - ran this on the test servers for a bit and it was quite a fun, but I didn't find it as enjoyable as my bot/dark tbh
http://www.scene-and-heard.com/cov/covsig.jpg
I asked this awhile back in the brute forum and got a lot of responses and since the MM is my favorite archetype even though I gotten any past 32 (lol), I wanted to ask here also now that im back to play again.
My question is what do you think is the best combos of primary and secondary if your only gonna play each once? Im having a hard time deciding and I dont wanna play each secondary more than once or primary.So far the only one im set on is demon/thermal.
Im also having a hard time picking a secondary for ninjas which is my favorite primary cause im a huge martial arts/ninja/sword type stuff buff. I'm looking for whats the best pairing for the other 5 sets. Thank you for all your ideas.
Edit:Oh I should say best for overall utility and aoe/st/whatever else. I like to be able to do it all but not be the absolute best at it.
I will remain a soldier until the war is won.