An alternative for controlling parasites/minds/whatever is that they only take control when the person's conscious mind isn't in control, so when they're asleep, knocked out, under the influence of narcotics etc. Might be a nasty surprise for the players to knock someone out, and the next second, they're up and swinging.

There's also symbiosis, like the Trills from Star Trek. In one of the novels, Jadzia gets shot in the head, and the Dax symbiote takes over control of her body for a short while, until it too gets shot (but it all gets undone via time travel).

What kind of situation are you thinking of - a single race that's dealing with people on earth for their own reasons, with maybe one or two of their rivals trying to upset those dealings, or a more open-Men In Black-type situation with earth playing (sometimes unwitting) host to refugees, exiles, wanted criminals and so on from different species?

Other possibilities: humans taken in the past for some reason and potentially modified (the populations of various planets on Stargate, Farscape's Peacekeepers), shapeshifters (Odo from DS9, Maya from Space:1999), silicon-based (Eldrad from the classic Dr Who story Hand of Fear, or the Horta from Star Trek's Devil in the Dark), or possibly species that can thrive in environments hostile to native lifeforms.