I mostly agree with xivarmy.
One or two Medusas can be useful to take out a single steathy unit, leaving the rest to be handled by Turturrets or Rocket Troops. But expect the Medusas to die very quickly. Medusas will not survive to the second wave of a two-wave battle. So they're useless against stealth in the second wave.
Mantas are pretty much there to annoy you when you have to fight against them, but they're not particularly effective to use. Sub Cruisers beat them always with the greater range.
Nautiluses (Nautili?) are ridiculous. If a Porsche and a Kia were the same price, you'd never buy a Kia. (In case it wasn't obvious, The Nautilus is the Kia, and the Sub Cruiser is the Porsche.)
CRABs are useful only against slower-moving stealthies and flyers. The unit that was "intended" to be the anti-stealth unit is less effective than the Scimitars.
Scimitars I have found to be quite useful against stealthies, such as Eels. With their high speed and immunity to retaliation, and occasionally hitting multiple units at the same time, they make a great compliment to Turturrets.
Eels are theoretically useful, but even vs an army with nothing that can hit stealth, you can usually get the job done faster with Turturrets and Sub Cruisers. Eels are sort of like the Mantas - there to annoy you when you have to fight against them, but not so great to use yourself. Put one or two in your defending army, to prevent people from attacking you with all Turturrets.
Octopi can be useful against Scimitars and Eels, when there are other units you can shoot at. The scimitars rush up to your units, so you then position the Octopod next to multiple units, and then shoot another - doing damage to many units at once. Put an Octopod next to an Eel and fire at something else, doing damage to the Eel without taking retaliation. But yes, it's very dependant on the situation.
In OF, Turturrets and Sub Cruisers do at least 90% of your work. If there are a lot of stealthy units, substitute Scimitars for the Subs. If there's only one stealthy, maybe throw in one Medusa or two. Most of the time, I use 4 Turts and 4 Subs. Most of the rest of the time, I'll use 4 Turts and 4 Scims. And Most of the rest of the time, I'll use 4 Turts, 2 Subs, and 2 Scims. On rare occasions, I'll use 1-2 Medusa, Octos or CRABS.
In VF, the Rocket Troops are the obvious most useful unit - the direct sequel to Turturrets. Ronin Bots are a good, solid workhorse to hit those flyers.
Ninjas are rather unimpressive. Rapid deployment is nice, but there aren't enough forests around, and the Ninjas either don't have enough movement to get to the nearest one, or when they do, they don't have enough range to hit anything once they're there. They combine the weakness of the Medusa with the weakness of the Manta.
Augmented Samurai should be renamed "Retarded Samurai". They belong in the same "Don't call us, we'll call you" category as the Drummers and Color Guards. And IIRC, there's even a Story Quest that *requires* you to build a Dojo for them. OK, so build it, but don't bother unlocking the third slot.