I haven't completely decided what I'm going to do with alignment in my Swords & Wizardry game. (Which could really use a name, but more on that later.) The system, by default, doesn't make any specific requirements about how or whether alignment functions, and though it does have a couple of suggestions the document makes clear that it's up to the particular referee to decide.
I've never done a whole lot with alignment in my games. My long running games both used d20 Modern and Arcana Evolved, neither of which even have alignment in the D&D sense. Even on the occasions I've run straight up 3rd edition D&D, alignment has never been that big a deal. Mostly, I just accepted it as either part of the game or not, and didn't give a whole lot of thought as to how I was going to include it.
With this game, though, it seems to merit a bit of consideration. On the one hand, at some point I would like to "do something" with alignment, make it and deities generally more important in a campaign. I'd really like, at some point, see about taking the Law/Chaos axis as far as it could go, to the point where the Lawful Evil and Lawful Good deities team up against all the chaotic ones.
On the other hand, I don't know if this is really the game for it. I'm trying to go for more of a pulp/weird science vibe with it, and I don't feel like big cosmological conflicts really fit. Feels too high fantasy. From that angle, since there's no mechanics regarding alignment that I have to account for with the system I'm using, I might just drop the whole thing entirely. Because if I'm not going to have a big cosmological set up backing it up, I don't know that it's worth the arguments and hang ups that tend to come along with alignment.
On yet third hand, the hand we use to talk about mutants, there is the whole radiation thing. The Gamma Knights, and their likely radiation and mutation worshiping adversaries, suggest an interesting angle of their own for dealing with "alignment" and similar things. The problem with that is one of terminology. "Pro-radiation" and "anti-radiation" are a bit awkward as entries on a character sheet, and they don't completely encompass the distinction I'm thinking about, since the Gamma Knights use a fair amount of radiation powered technology themselves, they're just careful about it.
And, of course, I'm not really sure what the point would be, in setting up a system more complicated than a detect radiation spell and a few other things of that nature. The fight against those crazy mutants up in the hills, exposing themselves and anyone they can kidnap to radiation, (or, alternatively, those stuck up Gamma Knights who think they know what's best for everyone, and won't let "the common people" in on the ancient secrets) may end up being a big deal within the campaign. But I don't know that I really need to systemize it.
Which would mean, then, that I'm leaning away from using alignment at all. That's very likely what I'll end up doing, but I have this sense of alignment as fairly important for D&D, which is still what I'm trying to play, even if a fairly modified version of it. I don't plan to discard it without some serious thought.