The Sky
The Sky
[Cueball and Megan are standing looking upward with in a small frame a light blue background.] Cueball: I like the sky. Megan: Yeah.
[Zooms out to show a blue evening sky, the sun must be setting to the left and a streak of yellow and orange clouds goes from top left to bottom right. The sky/clouds get darker further to the right and several stars are visible behind the clouds on the indigo blue sky in the top right corner. There are also some gray clouds low over the horizon. Cueball and Megan standing to the far left Below them and the sky from the horizon and down there is a thick a black slab taking up about a sixth of the frame height.] Megan: It's one of my favorite halves.

In this comic Cueball and Megan admire a majestic sky on a beautiful day.
This is one of the few comics where the scenery is drawn entirely in color, adding to the feeling of awe and natural wonder. The lighting on the clouds and the night sky in the upper corner suggest that this is either at sunset or sunrise, with the sun at the horizon outside the left part of the image. The picture is drawn to show the ever changing beauty of the many different stages of the sky rather than to be 100% realistic, as it would not be possible to see stars as clearly as shown, if the sun is still illuminating the clouds in front of them. When the sun sets or rises the light produces many different colors which can often be breathtaking to witness.  The pouch shaped cloud formations are called mammatus clouds and are usually associated with nearing of bad weather.
The comic, however, already start in a small panel, with uniform sky colored light blue background, above the large drawing described above. In this image Cueball says to Megan that he likes the sky and Megan agrees. Megan first elaborates on her feelings in the large image where the zoom out is so large that they have both become small and insignificant characters in the bottom left corner, dwarfed by the sky and cloudscape, with the ground a broad dark band beneath them.
Megan makes a statement about the sky: It's one of my favorite halves . She thus indicates that she has more than one favorite halves. As there are only two halves this thus implies that Megan likes both halves, i.e. she likes everything. Her statement is thus a tautology because it implies that the other half is also a favorite and there are no other segments that would not be among her favorites. There are several xkcd comics about tautology, e.g. 703: Honor Societies , 870: Advertising and 1310: Goldbach Conjectures .
In 1368: One Of The one of is also used in a similar way as there is really no other that that one in that comic, whereas here there are no other that has not be included. A very similar sentence is also used in the title text of 1524: Dimensions where the sentence, I would say time is definitely one of my top three favorite dimensions . This also makes very little sense as there are four dimensions with time, and the other three are indistinguishable as they are just three randomly chosen but orthogonal directions in space.
Taken at face value, given that the image depicts half open sky and half clouds, the other half could be taken to mean the clouds covering half of the sky. Or it could be the sky and the dark Earth, the other half beneath their feet. That it is the latter becomes evident in the title text.
In the title text Megan continues her comment as she states that her other favorite half has some cool objects in it. 
She then lists three types of objects:
From this it is thus clear that it is not the clouds vs. the sky she's referring to but rather the sky vs. something down on Earth. Weather the clouds are considered part of the sky or just blocking the sky could be something Megan and Cueball would disagree about. See below.
Based on these three items the other half could either be the entire Earth , just the solid ground or only the oceans . All three mentioned objects can be found both on land and in the oceans. Shipwrecks may be associate with oceans, but they are also often stranded on the shore. Snakes are mainly associated with land, but there are several snakes that live in the ocean. But the last part of the title text takes both the ground and the sea out of the equation, as it states that if those three objects where moved out of the way the other half would also have more sky. As Earth is round (and made from rock, most of them melted in the outer core ) then if you "moved all those rocks out of the way" you would see the sky below on the other side.
This leads to the realization that the two halves are indeed the Sky and the Earth (or Heaven and Earth). The title text is thus a subversion as it may be switching the readers focus of what the other half may be, as seen from only the large image (clouds, stars or the ground).
Beyond the blue sky above there is just the dark night sky of outer space . If it where not for the Earth the blue sky would not exists as it is formed by the air following the gravity and curvature of the earth. So if you would moved the entire Earth out of the way you would also move the blue sky with it and you would only see a similar dark night sky, with lots of stars like those in the top left corner. Of course if it was not the entire Earth, but just those rocks directly beneath Megan that was moved, then in principle she would be able to see the blue sky on the other side of Earth, But as she is saying moved all those away , it indicates that Megan really means the entire Earth.
This last part of the title text thus shows that Megan may be thinking rather of the night sky, and given that there are also stars visible in the top right corner, she could have assumed Cueball also referred to the sky like this rather than the majestic display of clouds and colors. Of course that would be weird, but that's where the comedy occurs because that was unexpected, and it would be typical Megan and/or Randall .
If Megan is also interested in astronomy then she would prefer a dark cloudless sky with stars. And by focusing on the fact that if the Earth was removed there would only be dark sky (empty space) around her on all sides, this may be one of her other often seen strange preferences. (Those are often used by one of the characters in Randall's comics). It is well know from xkcd that Randall really loves astronomy and looking at the night sky. So seen from this perspective, there would still be plenty of sky even if the Earth where removed completely. However, there would not be any clouds or nice colors or any humans or other lifeforms around to admire those astronomical objects.
The title text also indicates that although the other half also is one of Megan's favorites, it is mainly the shipwrecks (the oceans) and the snakes (life forms) that she considers when thinking of this half. The rest is just rocks (the Earth). Taking into account how many different things that are on "that other half", why did Randall then choose to mention those two? Only he will know, but maybe indeed to focus on the oceans and their life forms or any life.
[Cueball and Megan are standing looking upward with in a small frame a light blue background.] Cueball: I like the sky. Megan: Yeah.
[Zooms out to show a blue evening sky, the sun must be setting to the left and a streak of yellow and orange clouds goes from top left to bottom right. The sky/clouds get darker further to the right and several stars are visible behind the clouds on the indigo blue sky in the top right corner. There are also some gray clouds low over the horizon. Cueball and Megan standing to the far left Below them and the sky from the horizon and down there is a thick a black slab taking up about a sixth of the frame height.] Megan: It's one of my favorite halves.
