Chief and Anders were long pegged as cylons by fans, though, it wasn't exactly planned. Both had hints, which could have been incidental, led to their choosing, or some of the later ones on purpose. This is a copy past from what I wrote to bosk1 summarizing the four and their hints...
Tyrol: Some people thought his relationship with Boomer gave hints, I don't buy it. Cavil at the end of Season 2 says he fears he's a cylon. The Temple of the Five was his coming out party. Then he withstood the vacuum way better than his wife, in case you missed the Temple.
Anders: Anders survived pneumonia with no antibiotics and terrible living conditions with no explanation. Not unthinkable, but a cylon would have much better odds than a human of doing so. His groups continued survival on Caprica would have been a handily explained if they were 'normal' cylons. This had helped make Anders a popular guess, though. The giveaway was Caprica Three's apology. She had meaningful screen time with three humans, Baltar, Cottle, and Anders. She tortured Baltar, but was at that point his lover. He was also soundly shown to be human an episode or two later. Cottle there wasn't anything to apologize for. Anders, she tried to murder face-to-face.
Tigh: The loss of his eye might have been symbolism. Otherwise the only possible hint is by close association with the other two in the resistance. I think they probably weren't thinking about him until late, but those two things played nicely.
Tory: Nothing that I know. I guess they just needed another one and didn't know what to do.
Bosk1 firmly disagrees with me regarding Anders and the apology, he thought it was for the torture of Tigh, I believe. There's a lot more to this, but we have to wait until later to discuss it due to spoilers. For now, I still hold that it meant Anders, with tv I think it had to be a direct connection to something on screen, so Anders was the only choice.
There really wasn't a lot, but of those four two had been pegged by fans. There's been no confirmation how long anyone thought about these characters, but the final decision on them were late. At the very, very, least, Tyrol had to have been know mid way through season 3 even though they've never said so. I think they suspected where they were going with him by the end of season 2. Fans suspicions on hints may have also led to their choosing, since they were starting to fit in people's minds, who knows. We know they weren't really absolute hints set by the show producers, but again, this is better discussed later to avoid spoilers from season 4.