The most obvious evidence of cell theory is to look at cells themselves. Some cells are large enough to be seen with the bare eye; amoebas, for example, can be seen with a backlight. Using a magnifying glass or a microscope, even more kinds of cells can be seen, such as plant cells and skin cells. Some, like red blood cells and bacteria, are even smaller.
More evidence can be found in the behavior of a cell on it's own. An individual cell can be alive without the host body in the right conditions, and with microscopes these can be seen.
Further, cell replication and organelles can be seen through microscopes. Onion skin cells are commonly used to show cell replication, and some algae have easy to see organelles.