I am making pixel art for a game. I don't think I want to have the tree to be any more complexed and I want the look of bright green leaves. The style of the artwork I was planning to have is simple. I did look at reference pictures of trees, but the artwork would look very complex if I did it that way.
You seem to have a common misunderstanding about references. References are there for your understanding, not to directly copy. When you look at a reference and it's too complex for what you want, you simplify it-- for example, when you look at a tree, you can often simplify it into a few spherical/ellipsoid forms, with a series of tapering cylinders for the trunk and major branches.
One technique used for this is to squint, so the image becomes vague and blurred, and you only perceive the broad major forms involved.
With a good understanding of form and a good reference, your current rock, tree, etc could become much simpler than it is AND much more believable.
Do you reference real world images or pixel art?
Real world, in general. Referencing art is something that needs a good deal of caution, understanding, and double-checking (otherwise you could be copying someone else's mistakes).
And do you have a reference image for very piece of art? My game has unrealistic aspects in it and I want to be able to draw without reference.
You might have multiple reference images for any given piece of art. Thinking of art as being like making a collage, is good to illustrate how you find different qualities you like in different references, and combine those qualities you are looking for into your final artwork. So I would say, no matter how unrealistic what you want to do is, there are many, many possible references you can use for it, and using them will help make your final work more consistent and interesting.
To be blunt, drawing without reference is MUCH MUCH harder than drawing from reference, it requires you to be much better at the fundamentals of art, than drawing from a reference, and this remains true no matter what style you're going for.
In my experience, trying to draw without reference, while lacking those basic art skills, leads to lots of poking and prodding, hoping something ends up looking right, but not really knowing what would make it look right. ie. a huge time-sink.
re: dark parts:
The dark parts that yaomon adds to his example later are adding detail to the form for greater interest; this is generally known as modelling (you can also see modelling being added in the example Cyangmou posted). He is carving away some parts and building up others -- sculpting the basic forms he started with. Episode 3 in Moatdd's Youtube playlist
The Basics of Digital Drawing and Painting does a good job of explaining the basics of modelling.
re:unzooming:
Not sure what you are using to make your images, but any decent free image editor, for example GIMP, should have a 'scale image' function. In the case of GIMP, this function is found in the Image submenu on the menu bar.
In most programs, in addition to letting you select the new size of the image, you have a choice of 'interpolation method' or something like that : for pixel art, 'None' (or 'nearest neighbor') is the correct choice.