The ending sequence first appears in Episode 3. Remember that maybe what's shown in this ED won't actually happen in the anime itself, like the opening suggesting it's a happy-go-lucky magical girl story while it isn't that happy.
The light of love
The ending begins by a spiraling view on what appears to be clouds, that then turn blue
while the camera pans down to a view of the "horizon" while Madoka's silhouette appears.
Someday the light of love you hold within your eyes will transcend time
and certainly destroy a dream of a world racing towards its ruin
Sayaka's gesture can be interpreted as a feeling of guilt, which may be refering to how Sayaka along with Madoka decide to not to become a magical girl, but changed her mind later by herself. It can also suggest Sayaka's eventual falling out with Madoka over the latter's "failure" to become a magical girl and take some pressure off of her, as well as the fact that the two friends never truly reconciled before Sayaka's death.
Kyoko's position is ambiguous: she may either be looking down the path Madoka is walking (possibly referencing her "alliance" with Madoka in episode 9), or may be facing Sayaka due to her love for her. She is notably the only girl in the ending to be drawn in such a way, which may be an indication of the gray areas she occupies in the series: Kyoko is alternately a sadistic antagonist and a noble protagonist, with a materialistic worldview underscored by more intangible beliefs in truth and justice.
Swallow down your hesitation. What do you want?
With the direction this desire is going into, will there be a fleeting tomorrow?
Madoka passes by a sitting Mami, and then by Homura, who then reaches for Madoka.
Notice how Mami is, contrary to all others, not standing. It's most possibly symbolism for her demise.
Then Homura tries to reach for Madoka, as she's doing in the series, not with her hand, but with her words.
Racing towards destruction
Madoka starts to run as her clothes are ripped away.
Black lines are also going across the screen vertically as this is happening. This could show how darkness is slowly destroying Madoka. It could also be a poke at how this anime is destroying the traditional magical girl image.
I run alone
Like the ancient magic I saw in my dreams when I was young
With a power to crush even darkness, I want to see your smile
Madoka runs towards the light, and when she comes near it, it fades away, leaving only darkness.
Madoka has left everything behind to follow that light at this point. Her friends, and her magical powers (costume) are no more. But the light was just an illusion. Only darkness awaits Madoka.
Also notice how the darkness of these frames is similar to scenes in the last episode that had visualized hope and grief fighting with each other. The screen turns a bright pink (hope), before it is taken over back a big, black cloud (grief.) This could possibly symbolize how Madoka is running and taking control of all the hope and grief she creates.
In this shivering hand is the courage of a hand-picked flower
My feelings are all that I can rely on. Awakening the light is my wish.
As it gets darker, she actually loses all her clothes and then starts running as fast as she can.
Still, as she's running, she becomes a beacon of light in the omnipresent darkness.
Notice that this is the first time Madoka has stepped off of the glowing platform she has been walking on the whole time. She has finally left her safe world and is running towards the darkness, yet she herself is a sign of hope.
The eye of the mask
Finally the whole screen gets engulfed in darkness and we can see Madoka's silhouette in the eye of what appears to be a mask.
In the end, Madoka's stuck behind the witch's mask. The mask bears a passing resemblance of the cover of the movie Mephisto directed by István Szabó. Compare also to Baron Ashura of the Mazinger Series. Compare also with the image of Über Gretchen
It's also not unreasonable to speculate that this could be showing Madoka's eternity as she is trapped. She is always in the witch's eye because if she should ever stop fighting witches, her own witch will awaken.
However, Madoka in the Eye itself looks somewhat like Star Child, possibly foreshadowing the ending of the show.