Proper Method to Update WordPress is a consolidated guide to manual or automatic update WordPress. If you follow this methods nothing will break after update. The reason for writing it is, on the day of release of WordPress 3.5, it appeared to me, many WordPress users lack the basics.
Proper Method to Update WordPress : Official Documentation
Proper Method to Update WordPress Officially can be found here :
Other than update, there is actually a big documentation on WordPress :
Apart from that, we all are contributing to make a handbook for the average WordPress user. You can also join and contribute. Apart from the officially written ways for Proper Method to Update WordPress, we are adding some quick tips here.
Proper Method to Update WordPress : Follow the sub header of the doc
This is not a substitute or shortcut way that describes the Proper Method to Update WordPress over the official docs. Some points might be added there later, you must tally the sub-headers described below with the doc.
Check Requirements : We have a WordPress Compatibility Checking Script for Your Web Server. Do not run beyond the first step. It is coded in an way so that the first will itself do no harm but will only check your server.
Take a Backup : We have a simple plugin (it needs no installation) named FTP to ZIP. This to take the backup of your FTP folder. Apart from that, please take the backup of MySQL database through PHPMyAdmin manually.
Disable Plugins : Clear the cache, if needed clear manually from FTP. Disable the Plugins, specially the plugins which are related to Database cache or writes data on database frequently.
Normally this should never create any problem if you follow these three steps for automatic update.
Regarding manual update, every tit bits are written, even Subversion update is written. Most do not understand a basic thing, that there is no actual data on FTP, except the wp-content folder, wp-config.php, .htaccess etc. files, practically all are same for any WordPress like this one or yours one. The data is on database.
Host matters, PHP memory limit matters. But these are the basics.