In the Temple of Five, #3 (D'Anna) seeks to see the faces of the Final Five. Cavil says "That can't happen" and tries to shoot her. Later she is boxed for her quest (and also because the actress is only contracted for so many episodes, but we'll ignore that.:-)

As she enters the projection, she looks with some surprise at the 5 robed figures laid out before her. Curiously, there are six drapes, but they stand on only 5 of them, leaving the one on her left empty. Then she approaches one with a look of shocked recognition and issues the apology:

You... Forgive me I...I had no idea

(By the way, in a nice irony, as she gives up everything to see the faces of the Final Five, two of them are outside, getting shot at by her own Centurions.)

There was much debate before the end of the season who she recognized and apologized to, and there is still debate now even with 4 of the final five revealed. Here are some thoughts

• She planned a war that wiped out everybody's homes, families and planets. So she can certainly apologize to just about anybody. That doesn't tell us a lot.
• Anders: She beat him up on Caprica, and was going to kill him. In addition, her forces outside are shooting at him, and just shot down his wife's Raptor and she's seriously injured.
• Tyrol: Likewise, her forces are shooting at him. Also, she put his wife's name on a death list and almost got her killed.
• Tigh: While Tigh's torture seemed more a Cavil affair, she has some complicity in it, the loss of his eye and the loss of his wife. And Tigh, as 2nd in command of Galactica, reveals that the fleet she has been chasing is probably doing the will of the Final Five she worships.
• Tory Foster: Very little specific

In spite of all of these though, I think there is reason to suspect the apology is being made to the unrevealed member of the Five, whom I refer to as #1.

She would of course expect the Final Five, in human form, to be infiltrating the fleet. After all, there's effectively nowhere else they could be at this point. So recognizing fleet members should not invoke the heartfelt "I had no idea." Though it is possible, even easy, to interpret this as simply an extension of the apology.

If, however, it is truly an expression of shock at a grand agenda that has been suddenly revealed to her, this points to the missing #1 being one of the "big 3" -- Adama, Roslin and Baltar. And the next thing she does is tell Baltar that "you were right." It seems that only seeing one of these three characters would reveal to her that she really had no idea of what was going on.

By the time she is reborn in her tank, however, she seems in no particular rush to tell Cavil of her great revalation. She only tells him she would do it again, and there are "five other Cylons" which he will see "one day, one day." Curiously, he has already seen 4 of them, and has given an intense personal attention to both Tigh, and Tyrol. (Amusingly, when Tyrol asked if he was a Cylon, Cavil responded, "You aren't because I'm one and I haven't seen you at the meetings.")