Fontaine (Level)

One tip to remember... Save the game before you enter the elevator to confront Fontaine.

This is the point in the game where you fight Fontaine. The game autosaves before you step out of the elevator. After you beat Fontaine, the ending differs depending on whether you rescued or harvested the Little Sisters.

Trap Bolts are very effective against Fontaine, as is Electric Gel. Using the grenade launcher will help a lot as well. To the left of your entrance there is a healing station. There is also a bot shutdown panel next to Fontaine's chair. To kill him, you must inflict damage upon him until he runs to recharge his atom and then while he is open for attack, you must run up to him and suck out his atom with a little sister syringe, you must do this four times before you beat him.

After he is dead, Jack returns to the surface after an undetermined amount of time. After this, there are three possible endings based upon your actions prior to it:

If you harvested, i.e. killed more than one, but not all, of the Little Sisters somewhere in your journey, Jack will turn upon the Little Sisters who killed Fontaine, and we are to believe he harvested them for their ADAM. After this, the cinematic shows a submarine coming upon the wreckage of the crashed plane that you were in, but it is soon surrounded by Splicers who kill everyone in it and take control of the submarine. All of this is narrated by Tenenbaum's voice as she condemns Jack for his actions.

If you harvested (killed) every single Little Sister you came upon, then you see the same cinematic as above, but with an angrier narration by Tenenbaum.

If you rescued every Little Sister or if you only harvested one Little Sister throughout the game, then you see an alternative ending. The cinematic shows a bathysphere surfacing by the very lighthouse you entered Rapture in; this time, it is in complete daylight. The door opens, and you see that it is filled with rescued Little Sisters. Jack helps them out, and the cinematic proceeds to show them living happy, fulfilling events in their futures, such as graduation, marriage, and parenthood. The cinematic ends showing Jack on his deathbed surrounded by some of the grownup rescued Little Sisters. This is a heartwarming cinematic, and is narrated as such by Tenenbaum's voice.

Nitpicking
Regarding the ending you get if you harvest any Little Sisters: It is very odd that Jack would decide to harvest the Little Sisters at the end, even if he had been doing it the entire game; from their normally-colored eyes and their healthy skin tone, it is very easy to tell that the Little Sisters who kill Fontaine were the sort who no longer have the ADAM-producing sea slugs in them. This would mean that they would have very little ADAM left inside them, if any. Perhaps Jack, like the Splicers, had used so much ADAM that he was now not only addicted to the substance, but mentally unstable as well, and he was willing to kill the Little Sisters on even the smallest chance they might contain some ADAM.