In order to pick up and item from the ground, you need to get fairly close to it (more or less at arm's length) and aim at it until one of the icons appears:
This icon represents miscellaneous items. All kinds of items found in the game can be among them - for ammunition to food.
You will see this icon if the item pile contains only weapons and/or ammunition.
After one of these icons appears on screen, press [G] to open the inventory window. You can also use the mouse wheel and choose to "pick up item x". However I don't recommend such a method, as using it you cannot move your items to the backpack to make room for others.
After opening the inventory window, you will see that on the list on the left side, apart from the items that you already have, the ones from the pile will also appear. The column on the left (red) there's the number of items of each kind in the pile on the ground. The column on the right, on the other hand, shows the amount of items that you have in your inventory (but not in the backpack).
In order to take an item from the item pile, click the right arrow (green), found beside the marked item. Similarly, in other to place the item in the pile, press the left arrow (red).
Remember that if all of your slots of a given kind are empty, picking up another item will result on throwing out one of the items from that slots that you already have. Proper slots are highlighted when you choose an item which can go to them. That rule doesn't apply to tools, as you cannot take more than one of a kind and there aren't that many kinds of them in the game yet to overfill your tool belt.
Picking up a main weapon, you will also gather the ammunition for it (assuming it's in the same pile). If you already have a main weapon and wish to change it to a different one from the pile, ammunition from the old one will also be thrown out.