Well, since we're talking about a lore element already revealed in
Mass Effect, I guess it's pretty safe to talk about it without spoiler, so that maybe even the others can chime in and tell their opinions.
The
Genophage. It's a really tough question. Of course, such a weapon is morally questionable. Better yet, if looked from a strictly ethical perspective, it's just downright wrong with no redeeming possibilities. As one of the (very, very minor) characters in ME2 puts it, it is a
cultural genocide, even if not a physical one, and I strongly believe that it's possibly worse. As a person, in real life (yeah, I know: I'm talking sci-fi here

), I'd strongly oppose anything with even a slight resemblance to such a horror and the very thought of being able to destroy a population with this subtle and yet lethal method sincerely creeps me out. It's wrong, and abusive.
Still, if I try to put myself into Shepard's shoes and think like an in-game persona, I can see why the Genophage was planned. While I still find it morally despicable - and I roleplayed Shepard accordingly -, I can see why the Krogan's uprising could have easily resulted in the destruction of the entire galaxy. Was couldn't solve the situation (Krogans were too many and too strong), and even the Turians couldn't stop their fleet. Entire worlds were succumbing to their restless fury and entire colonies were annihilated. Something ought to be done.
Was the Genophage the best answer? I highly doubt that, and if a cure were possible, I'd like my personal Shepard to anything in his power to find and apply it. However, the Genophage at least stopped the war right away, saving countless worlds, colonies, settlements and so on. Only the Krogans paid the price, true, but, on the contrary, if they weren't stopped, the entire galaxy could have paid it. Perhaps it was inevitable.
Now, though, a solution must be found and the Krogans must be helped into a sort of Renaissance era, an Age of Enlightenment, perhaps, something that can help us dominating their supremacy instinct and finding other (peaceful) ways to integrate with the rest of the universe. When this cultural enhancement has been achieved, the other species must done everything in their power to solve the Genophage problem, maybe devising some other containing method (arms embargos, for example; or some sort of taxation).