I was wondering what is the best way to store a users upload images like an avatar and so on using PHP and MySQL? Where should I begin? And is there a good article on this?
"Best" depends on what your goal is.
The two primary ways of storing user-uploaded images are either putting the binary content into the database as a BLOB, or storing the images to the drive somewhere and putting an entry into the database indicating which image belongs where.
Placing the images in the database has the advantage of not requiring any sort of filesystem permissions on the webserver, and removes any sort of syncing issues if you're serving up the site off of multiple webservers. However, over time it makes your database huge, and if you don't design your tables correctly, it can absolutely kill your performance and scalability.
Storing the images as file on the file system has the added advantage of making retrieval extremely quick and efficient, since webservers are very good at serving static files.
Edited to add
If you decide to store file content in the database, absolutely do not put it in a table that needs to be accessed quickly. If, for example, you have a "users" table that is searched on nearly every pageview, then that table is not the place to put your file contents. Instead, create a separate "images" or "files" table containing the file and related meta-information.
Putting a lot of bytes per row into a table makes that table very slow to work with. You don't want that kind of thing in tables that see heavy use.