$UserBaseDirectory/Kernel/init.m

Make a symbolic link from a version controlled init.m to $UserBaseDirectory/Kernel/init.m. It 1) defines some environment variables such as

SetEnvironment["$DropboxDirectory" -> FileNameJoin[{$HomeDirectory, "Dropbox"}]]

and 2) loads some packages that I use frequently enough that loading them every time is convenient:

<< meng` 

$UserBaseDirectory/SystemFiles/FrondEnd/Stylesheets

Make a symbolic link from a version controlled directory of stylesheets path/to/Stylesheets/ to $UserBaseDirectory/SystemFiles/FrondEnd/Stylesheets so your own stylesheets is readily accessible from menu Format > Stylesheets and you can keep them update-to-date with its version control repository.

Install SSL certificates

Sometimes, in order to operate with some Web sites with functions like URLFetch, additional SSL certificates associated with the site needs to be appended in

FileNameJoin[{$InstallationDirectory, "SystemFiles", "Links", "HTTPClient", "SSL", "cacert.pem"}]

This will allow HTTPClient to use the SSL certificate for authentication.

FrequentlyRunCommands.nb

I have a notebook where I record all the frequently run commands for quick reuse. It can be set to automatically open when Mathematica starts.

• Format → Option Inspector
• choose "Global Preference"
• Global Options → File Locations → AutoOpenNotebooks
• Set value to "/path/to/notebook.nb"; separate notebooks by linebreaks

Preferences

Mail server

• Preferences > Internet Connectivity > Mail Settings.

Interface

• Preferences > Interface > Show open/close icon for cell groups

Uninstalling

See Wolfram documentation.

When having multiple versions installed, to uninstall one of them, delete

• /usr/local/Wolfram/Mathematica/VERSION

Replace VERSION with the version number you would like to delete.