The best thing to do would be to tell us what your primary is. Using that information we can suggest what would be best to slot in each henchman. 
atm thugs' but i might try nin or necro later
You can use any normal enhancement that matches your origin. (If you're not sure about your origin, go to Menu - Personal Info.) Also, hovering over the pet in the Enhancement screen will tell you which IOs and set types you can use.
Edit for clarity and example:
For instance, you're a Mutation mastermind. You can use TOs, DOs that share a Mutation origin, or Mutation Single origin (see wiki link below if you aren't sure what those are.) In addition, you can use any generic Invention Origin (invention: damage, for instance) the pet will take, as well as any set.
Looking here for instance (a Robotics MM) you can see that my Protector Bots can accept:
(generic)
Damage
Accuracy
End Reduction
Knockback
Defense
... and other IOs, as well as Pet Damage, Knockback and ToHit Debuff sets.
If I tried to fit another set that isn't listed (such as Miracle, a Healing set) in, it wouldn't take it.
lol luv that cat pic bill
MMs pets are fairly easy to slot. Max out the ACC with three ACCs (if you're using generics) in your tier one pets because later on in life they fight at two levels below you, so you don't want them to miss all the time. Then max them out on damage with three DAMs. Your tier two and three pets will have enough ACC with two, them max our their damage with three DAMs. That leaves you a slot on each for their various effects or needs; for instance, tier two Bots need help with END, so there's the slot right there. Or you might go for enhancing certain effects they have like stuns, holds, heals, whatever.
Now if you frankenslot with IOs, you can max out ACC and DAM in five slots on all three tiers as well as possibly worming in a few extras like the +END needed for bots. There was a really good thread about doing that that I no longer have marked because of the forum swap. 
I do have some notes though, lucky us!
To do this (if I can read my notes rightly), you need:
Unquestioning Loyalty 30th level Acc/Dam
Brilliant Leadership 30th level: Acc/Dam and Acc/Dam/End
Blood Mandate 30th level: Acc/Dam and Acc/Dam/End
They only need to be level 30 IOs to get the "maxed out" effect, but if you can't find a 30th and say drop in a 34 instead or perhaps a 28th or whatever, no prob. Just keep an eye on the math. 
The couple of times I've done frankenslotting I haven't really missed the set effects all that much - not that I recall any of the pet damage sets having much to go for in that regard anyway :P - and it's usually cheaper and a bit of fun figuring out the math to make your choices workable.
Other than that, just double slot you equip powers with two END.
That's how I've been doing it on my latest MM and it seems to work out pretty well. Hope this helps out.
Enhancements work on pretty straightforward tiers. Training Origins are considered placebos, Dual Origins are better than TOs, Single Origins are better than DOs, Invention Origins are about on par with SOs until level 35 or so, where they start getting better.
Ok so i just started and im not sure how too slot my henchmen what ones work what ones don't. like for dmg do any dmg enh work or just certain one's? Also what about other stuff like def and acc? Is there a guide out there that help tell you what enh too use and what ones not too i haven't been able too find none? Any info would be a big help.