Assume 4 v 4.

Seems like the team layout should be 2 offensive players and 2 defensive players. One guy watches the area where your flag sits (whether or not there's a flag there!) and the other guy hangs out in the base and continuously respawns your offensive team and protects your base from the other team blocking it.
Ok, it's a big deal that the guy protecting the flag stay there even when the flag is taken. Why? Simple, if the other team succeeds and runs it down, the flag will respawn there instantly. If nobody's there to defend it, and nobody notices it needs defending, the other team gets a free shot at picking it up again. Before you know it, the other team's run up their score quite drastically. So if you happen to notice that you don't have a goalie, take it, whether or not there's a flag there. I was able to turn the tide in a couple of rounds by doing exactly that. Sure, you lose 3 points by letting the other team get one flag back to their base, but that's better than giving up 30 points, eh?
So then you have a guy that sits in the base and keeps respawning your offense. This should be pretty obvious, but there's a catch. See, the guy protecting the flag needs to make it very clear that he'll kill himself when he's the only one left and the other team snags the flag. And he won't go and respawn his team, he won't try to save the flag. If he kills himself, he denies the other team the run. They can try, but chances are they won't get the flag back once, and then everybody respawns, right? Right. (Did this earlier and it turned a shitty situation into a fighting chance to win. We ultimately blew it, but we started the next round down by 1 point. No telling what kind of damage would've been done if I'd gone for the respawn) IF the other team knows that's the situation, and they're smart, they will respawn your team for you when you're down to 1 player. Because if they don't, they don't get any more runs that round. Some day the situation will be like this for everybody, I'm sure, and the respawning defender will be more of a wildcard slot where he can just go help as needed.

For now it seems to me like the guy protecting the flag should *never* go respawn his team. So if it's 3v3, you run 2 offensive players and 1 defensive player, and that defensive player only protects the flag, he never goes to respawn his team.
I think a good attitude to adopt is "I will respawn my team by returning victoriously to my base with the other team's flag".
Personally, I had more luck defending the flag by laying out a good-sized rectangle. Any time I tried a different layout, like an L, or whatever, I had a hard time maintining it. This was mostly because the lag bombs on that server are pretty nasty and it's pretty slidey. On a better connection, well, let's just leave it at that.
I found the easiest way to return the other team's flag to my base was by respawning their dead teammates right after taking their flag. The confusion that accompanies a fresh respawn is exploitable and usually results in a corridor relatively free of enemies. The only problem there is that corridor leads directly to your flag, where there's usually an enemy trying to get in. Still, you can at least try to distract him by waving his flag at him and heading for your base and potentially giving your defender a little breather, and he'll appreciate that.
Don't be afraid to respawn the other team!

Ok, etiquette.

If you intentionally kill a teammate, I guess it doesn't matter if it's nice to go respawn him or not.
And don't whine about wanting a respawn. I guess that's pretty well covered in another thread, but seriously, the best way for your team to respawn you is by bringing in the other team's flag, and the best way for them to do that is by not being contantly annoyed with "res plz lolz omg haxx0r" spam. Actually, after the suicide tactic sinks in a bit, you can probably get the other team to respawn you by just saying "suicide", heh heh.
What do you do when both flags are occupied? Personally I found camping in my base the right thing to do. For one thing it means I'm keeping my team spawned so they can attack the other team's flag bearer. If I get killed, the other team *has* to respawn me when they go to return their flag (along with any of my dead teammates). And the other team likely didn't leave a person defending their flag zone, so I'll respawn more or less in the clear and have an opportunity to go get their flag before they can get back to defend it.
The main thing, I think, is that offensive players need to know that if they return their own flag to base, it will be defended. I don't think it can be stressed enough that you should continue defending the flag's spawn point even if there's no flag in it!