Well, there's a few things they talk about:
1) Signs - they could be changing up the signs, particularly when you have a player at second base. As many teams (in particular, my Blue Jays) are adept at stealing signs, this is actually a relatively more common occurrence than you might think. Often this happens without a mound visit (when the catcher does a rotation with his hands, usually means they're switching to a new set of signs)
2) Situation - this is where often see the infielders come in to discuss as well. They discuss the current situation, their plan, and the defensive positioning based on the situation/approach. A good example is if there's a runner on base. You discuss who covers second, whether you wanna pitch out and how often, or even if you wanna hold him on. A lot of that depends on the score, the batter, the expected pitch selection, etc.
3) Batter - often they're talking about the batter specifically and a discussion of their pre-game plan against that batter and how it currently applies. As baseball is a constant game of adjustments, they may be altering things up depending on how the previous at-bats have gone or what the pitcher's pitches are like that day (ie. slider ain't slidin' well, curve ain't bitin', fastball moving a little more than usual, etc). If you see a pitcher waive off the catcher two or three times in a row, they're clearly not thinking along the same lines and need to discuss
4) Pitcher - if a pitcher gets flustered or is getting out of his mechanics (often something they've been working on) or whatever, the catcher (and sometimes pitching coach) will go out there and talk about the pitcher himself and what he's doin' and what needs to be fixed. This is very common nowadays, particularly if you have a veteran catcher. They don't even go out to the mound every time to do this, could just be a quick point or other hand gesture, like the sign changing.
5) Delay - sure, there are situations where there's a delay tactic going on, but you really don't see that much in the majors anymore. And the umps are all OVER it, that's when you see them walking up to the mound pretty damned quickly instead of giving the catcher/pitching coach some time to talk
In a general sense, that pretty much covers it
I was there on that fateful day, were you?