How the mu-plugins Folder Works in a Multisite Installation?

The mechanic is the same in Single and Multisite installations.

And yes, the plugins inside mu-plugins will be activated in the entire Network.

To enable a new thumbnail size in all the sites except the one with ID equal to 3:

global $blog_id;
if( $blog_id != 3 )
    add_image_size( 'category-thumb', 300, 9999 ); //300 pixels wide (and unlimited height)

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Reading the Codex we also learn that:

WordPress only looks for PHP files right inside the mu-plugins
directory, and (unlike for normal plugins) not for files in
subdirectories. You may want to create a proxy PHP loader file inside
the mu-plugins directory:

<?php 
// mu-plugins/load.php
require WPMU_PLUGIN_DIR.'/my-plugin/my-plugin.php';

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Just in case, I have this observation in my testing plugin inside mu-plugins:

// USEFUL FOR SOME STUFF THAT DON'T RUN IN THIS MU-MODE
add_action('plugins_loaded', 'brsfl_late_init');

function brsfl_late_init() {
    //add_filter( 'attachment_fields_to_edit', 'fb_attachment_fields_edit', 10, 2);
    //add_filter( 'attachment_fields_to_save', 'fb_attachment_fields_save', 10, 2);
}