Interesting question numbering. a, 2, d. Yep, you grew up in Alabama!
Here we go:
a) I have read vague comments about locked rooms. Whats all that about?
a) In past incarnations of the site, we'd sometimes have issues with poeple posting to games who were not actually players of said games. Even now, from time to time, this can happen... newbies mostly will post to a game they think is interesting, not realizing (or caring) that the game is only for those accepted by the GM.
Not too long ago, we made it posible to "lock" a game thread (either in the rules-based or freeform forums) to everyone but those specifically designated by the game's GM (aka the thread author). This is accomplished by choosing the thread type when you start it, or by editing your thread appropriately. If you need help on this, PM me or post here.
2) Is there a "standard" that is considered commonplace as far as play format around here? I see that timestamps are critical, and a generally good idea, what else?
2) Not really. Different GMs run games according to their own taste. Some games require nothing but one or two line posts "I stab the orc," while others expect novellas for posts (see the Star Trek games). Most fall somewhere in between.
Many games have no set posting structure, while a few (again, see the Trek games) have some fairly strict formatting.
Timestamps are a very good idea in games that allow for a lot of leeway as to when characters do various things, or when time might be critically important. In traditional "party-based" games - e.g. D&D - this isn't as big of a deal, since everyone is together anyway, and nothing much will happen until the GM says so.
In the oft-mentioned Trek games, a player is allowed to control not only their character, but multiple NPCs, which may be scattered all over a huge starship and/or a nearby point of interest (starbase, planet, etc). Without timestamps and locations, the game becomes impossible to read.
In my Cold Day in Hell game, I timestamp everything to the minute, but this is largely a style choice on my part, meant to help reinforce the structured, military flavor of the game more than anything else (and to give me some backup on a few rulings that might come up).
In my Guiding Light game, I post a header with the date, location, and approximate time of day, but nothing more. This is purely a cosmetic choice on my part, and really adds nothing to the game. I just like to do it.
The most important thing is to decide what you, as a GM, are looking for, and then to communicate this to your players. The point of this site is to have fun... it would be counterproductive to that if we were to force a certain format on everyone.
d) It seems that the in character game threads are overlapping in one gestalt thread. Is this the standard? How is game-critical information handled? For example, a scene in which one of my players is revealed to be a cylon agent... but only one crewmember is there... am I going to have to let every player I have see that scene? What is done in other games?
d) The norm is to have one main thread for the game itself, in which all players, as well as the GM, post. This is usually kept seperate from the recruitment thread. Also, it is frequently useful to have a Q&A thread for your game, so that players can ask questions or post OOC information without interrupting the flow of the game.
As for communicating hidden information, different GMs handle this in different ways. Some might post the cylon moment in the game thread witrh the understanding that only the player who witnessed it may allow their character to act with knowledge of the event. Good players would know to do this, anyway, but you can never assume.
Others might elect to PM or email the player involved, and to keep the secret information out of the game thread. This is also perfectly acceptible. In the end, the GM has full control of his or her own game. Whatever works for you, works for us.