There ws an episode where Troi had to take command after the ship was in an accident and she was the only officer there. (Picard was trapped in a turbolift with some kids) She was totally useless and O'Brien had to constantly tell her what to do.

I'm pretty sure that Scotty was formally 3rd in the command chain. Sulu was given command of the bridge a couple of times but I think that was only when Scotty was on the away team or otherwise occupied with keeping the ship from exploding. There were doubtless a few occasions where he was passed-out drunk like any good Scotsman as well.

it's strictly seniority in reality. the CO and XO are actual positions in the hierarchy, then it would be the department heads based on seniority. (we won't get into Command Qualifications)

Sulu taking the bridge was just Kirk's idea of developing junior officers.

One of my sailor friends is a 4th Officer on board a Dutch cruise liner so having Numbers 2, 3 and even 4 are perfectly fine on a large enough vessel.

Sulu may actually have been a department head, though. Possibly Operations? (I don't think this stuff was defined back then, though...)

The Second Office is one your department heads. As other have said it not position. It additional duty. General it senior ranking Department head.

Well according the great Memory Alpha

Link: http://en.memory-alpha.org/wiki/Second_officer

Also the page for 3rd Officer: http://en.memory-alpha.org/wiki/Third_officer

It says in regards to Deanna Troi

I'd assume she wasn't considered a normal bridge officer but seemed to be above Crusher by this point in the Chain of Command, but under Picard, RIker, Data, and La Forge.

From what a friend was was in the navy once told me, medical personnel are considered outside the normal chain of command and will only take charge in an absolute emergency; save on hospital ships where captains are usually physicians themselves. ST seemed to base its protocols on the British/U.S. model by and large.

But still would be nice to have a 2nd officer in command lol

I would not mind having designated First and Second Officer possitions. Beyond that, no.

Last I knew (correct me if I'm wrong), the main purposes of the XO (First officer) are to take the "short" captain's orders and "flesh them out" for the entire crew, and is designated to take command if the Captain is incapacitated.

"Second officer" is the guy designated to fill in as XO if either the captain or primary XO is incapacitated. Since this is primarily an "emergency" position, and space on a ship is at a premium, it's all to easy to envision the "owner" of this post as being a senior department head when not being third in command...

And what I mean by "flesh out orders of the captain", remember the older navy shows? The ones where the Captain says "all ahead full", and the XO makes sure that the helm/navigation knows what direction "ahead" is and signals the engine room to build up the engines for a full speed push? I actually vaguely recall Riker doing this a couple of times in the shows...

However, since we don't get to see our BOffs in action, and especially incapacitated, I'm happy to stick with designating my second in an RP sense and not having a formal option to do so... Now, assigning a BOff as "third shift duty officer"...