Sometimes I have a Taldan PC who outright states that Taldor is awesome.
The most secret I play it is at a "Joe and I will take this book for safe keeping -- wink wink, nudge nudge" sort of level.
At any rate, even if the other players don't know which faction you're in, having three players pipe up in unison "Are there any jeweled daggers in this room?" is a dead giveaway that some people are in a different faction.
I myself have never, ever resorted to: "Hey everyone, I need to harvest to undead parts in order to research a poison, er Antidote to a Poison (yeah, that's the ticket). If anyone happens to want to help me harvest some undead parts, I in turn will be quite happy to not watch what you are doing when you need to pass a note. I will also be quite happy to help look for boks, jewelery, pottery, or the like. I'm not saying I work for any particular faction, but if such a task were somehow to accomplish itself, I would not be adverse to such an occurrence."
Nope, never done that. Never. Ever.