First, we should start by stating that BackupBuddy will backup everything from the WordPress root and recursively down the file-tree. This means the directory/folder that your main WordPress directories are in (wp-admin, wp-includes, wp-content), BackupBuddy will backup that directory and down.
There are default exclusions that BackupBuddy adheres to as well, I will list them below. If you see files that are not on this list that you would like to exclude you can do so on the BackupBuddy settings page. You can find the exclusion settings at the at the bottom of the General tab, under the File & Directory Defaults settings.
/.itbub -- Our zip archive primer file on the offchance it is present
/.sucuriquarantine/ -- Infected files.
/wp-content/uploads/sucuri/ -- Temp files such as IP bans.
/wp-content/envato-backups/ -- Don't backup backups of other plugins.
/wp-content/backup-db/ -- Don't backup backups of other plugins.
/wp-snapshots/ -- Don't backup backups of other plugins.
/wp-content/ai1wm-backups/ -- All in One WordPress Migration backups. Don't backup backups of other plugins.
/wp-content/updraft/ -- Updraft stuff.
/wp-content/cache/supercache/ -- WP Super Cache temp data.
/wp-content/plugins/wordfence/tmp/ -- Temporary wordfence data.
/error_log -- Can be very large; server-specific and unlikely to need.
/wp-admin/error_log -- Can be very large.
/wp-content/mysql.sql -- WPEngine's stuff.
/_wpeprivate/ -- WPEngine's stuff.
Here are some things you should look out for that you may need to exclude within your own site:
1. Check the BackupBuddy site size maps tool. The site size maps are an amazing tool within BackupBuddy. This will show you a list of all your site's directories in descending order from largest to smallest. It will also highlight already excluded directories in red. This allows you to see the directories/folders that are taking up the most space on your site. Then you can go take a look at those directories through FTP/SSH and see what is taking up all the space. To go to this nifty tool, start by going to the BackupBuddy Server Tools page. Once there, click on the Site size maps tab. Now that you are on the tab, click the Display directory size listing button. This will show you all your sites directories in order from largest to smallest. Also, if you are using different backup profiles, you can select which one you want to use in the dropdown. This will allow you to see what is taking up the most space within your current backup profile. This is the number one way to see what is taking up space on your site and what could possibly be excluded.
2. System files. This means files such as php.ini, nginx.conf, debug.log, error.log, etc. Any files that pertain to the server environment the site is currently on should be excluded. These may exist within the root/main directory of your WordPress site. Though, remember BackupBuddy only backs up from your root/main WordPress directory and down the file-tree, so only worry about system files that exist within those directories.
3. Sites within subdirectories of your main site. Some sites have other sites within subdirectories of your main site. Remember how I said BackupBuddy backs up everything from your main WordPress root directory and down the file-tree? Well, that includes subsites if you have them in your main/root directory. So say you have your "testsite" directory/folder in the same folder/directory as your wp-admin, wp-content and wp-includes folder. Well, that will more than likely need to be excluded as you do not want to be backing up a whole other site! So make sure if you have extra sites within subdirectories of your main site, you go ahead and exclude those as explained previously in this article.
4. Backups made by other plugins. While we do have some backup directories made by other plugins added to the exclusions list, you will need to add directories added by other backups plugins to your default exclusions list on the BackupBuddy settings page.
5. Caching files. Caching files made by any plugin for any reason should always be excluded from a backup. You never want to restore old cached files as those could contain URLs to the site's previous location or could be just plain out of date. BackupBuddy excludes wp-content/cache by default. If you have a plugin that uses cached files, please have them excluded on the BackupBuddy settings page.
6. Files that are not necessary for the site to fully function. Some examples of this would be images or files that are not currently being linked to on your site. Since these files are not linked to by a file or a database reference, then it is okay to exclude them from the backup.
7. Files created by other plugins specific to your server environment. Plugins such as WordFence create a PHP configuration file called .user.ini, which uses an absolute file path that generally breaks on another new server due to the path change from one server to another.
In conclusion, exclusions will be different for each site because each site is different. So it is up to you to use your best judgment on what should be excluded on your site. Because the lighter and more free of junk your backup is, the easier it will be to move it around and import it.