Learn English – Apples are “in the tree” or “on the tree”

Your case is special. If you were to say two people were "sitting on a tree" in this case, it would imply that the tree was on the ground—i.e., that it had fallen or been cut down. Sitting "in" a tree means sitting in among the branches, most likely at least partly hidden from view.

Further discussion

I wrote the above eight years ago, and still stand by what I say. Nevertheless, there are nuances to everything. Consider first this stanza from W. B. Yeats's "Sailing to Byzantium":

That is no country for old men. The young
In one another's arms, birds in the trees,
—Those dying generations—at their song,
The salmon-falls, the mackerel-crowded seas,
Fish, flesh, or fowl, commend all summer long
Whatever is begotten, born, and dies.
Caught in that sensual music all neglect
Monuments of unageing intellect.

The poet is concerned here to draw a contrast between old and young, and the birds (in the fragment I boldfaced) are on the youth side of that equation. No place, there, for fallen trees; these are youthful, upright and leaf-covered.

Now, the leaves are probably the origin of the use of the preposition in with respect to trees: the birds are in among the leaves. Unless the foliage is sparse, you probably can't even see the birds, though birdsong may announce their presence. They are in among the branches, in among the foliage. Even on a leafless dead or dormant tree, though, we still refer to birds in the trees.

Note, however, that it is entirely proper to say that a bird lights on (or upon) a branch. There it is quite obvious we are close enough to actually see the bird in the tree.

Now, just to confound everyone (and reveal the nuance), consider another reference. This is from The Mikado by Gilbert & Sullivan, from the song "Tit-Willow":

On a tree by a river a little tom-tit
Sang "Willow, titwillow, titwillow"

This is a legitimate usage, one that would seem to contradict my statement about the in usage. But I don't think it does. Gilbert is offering a little sketch of a bird singing, and to do so it must sit on a branch. We're given a close-up of the bird, and the economy of words necessary to lyricize a simple song forces Gilbert to pare down the verbiage, so the ideas are telescoped: "On a branch of a tree" simply wouldn't scan. And had he used in in this case the focus would have been widened to emphasize the tree, not the bird—hardly appropriate to the song of a little bird.

This whole matter just illustrates once again how squishy and difficult prepositions can be in English—or in any language, for that matter.

Creak (“To make a prolonged sharp grating or squeaking sound, as by the friction of hard substances”) is the most-commonly-applicable term for sounds made by parts of trees moving in the wind rubbing together. An answer to Question380662 at theanswerbank.co.uk explains fairly well one of the sources of creaking:

... when the wind blows, and its force moves the tree, the tree does not move uniformly.

As a living organism, a tree is in a constant state of development, so the fibres in its trunk and branches are all at different stages of development - some are fully mature and dry, some are new and full of sap. As the trunk and branches move, different areas of the wood respond differently. Some move a good deal, some don't move at all.

As different fibres with different tensile strengths which are in close proximity react - or not - to the force of the wind, they rub against each other with friction. This is what causes the distinctive 'creaking' noise when a tree is bending in the wind.

Another common source of creaking is that different large limbs of a tree may curve and cross each other, thus making creaking noises as the wind moves the limbs independently.

Crack, crackle, groan, and boom are other verbs commonly used to describe tree sounds. Cracking and crackling often occur during cold snaps that freeze some of the tree's sap. Boom is used several times in a New York Times article about New Yorkers injured by trees or limbs falling on them. The article incidentally mentions some of the noises that occurred before the incidents; for example:

Mrs. Berger’s was among at least 10 lawsuits in recent years that have raised questions about whether more diligent tree care by the city might have prevented the crack — or creak or boom — and the death or injury that it brought.