If you have fan in the window blowing into the room it has less potential to multiply the air it takes, it will typically be also already IN the room itself which will greatly decrease its efficiency.
On the other hand if your goal is to cool yourself when sitting at the des it is generally better to place your fan blowing in, this means you can direct the flow of air to wherever you want. This means you can direct it at your desk to cool yourself by just the air movement alone. When you place your fan blowing outside you loose that ability. Blowing the air at you means you can cool yourself even if the air temperature outside is higher than inside!
If your goal is to move as much air through your room then you need to take into consideration the following:
- do you have other openings in the room (like doors... huh)? - can you have flow of air through the building -- typically there will be pressure difference between two sides of building unless the air is completely still
If you can have your door and the window open, observe the direction of air already naturally flowing. Then put your fan so that it blows with already moving air, for maximum efficiency.