Richard Vencu

This plugin creates and maintains one or multiple hierarchies of blogs in the WPMS network. Options screens appear in network admin dashboard. The blogs hierarchy can be used for several purposes such as:
<ol>
<li>consolidate posts (or latest posts) from descendant blogs only</li>
<li>display a list of descendant blogs or even a tree of blogs from any node</li>
</ol>
Other features
<ol>
<li>Hierarchy cannot loop (cannot set as parent one of the descendants or itself)</li>
<li>The main site (blog_id 1) cannot have a parent</li>
<li>Individual blogs may be taken out of hierarchy</li>
<li>Multiple independent hierarchies may be created 
Limitations: this plugin is not optimized for large installations. More than 50 blogs can be hard to manage.</li>
</ol>

Network Sites Hierarchy

This plugin creates and maintains one or multiple hierarchies of blogs in the WPMS network.

Amin Nazemi

This plugin disables Pagination in navigation menu lists and preserves taxonomy hierarchy. 
Also, it helps you when you using WooCommerce and you have more than 50 category items. 
It can preserve WooCommerce category hierarchy.
FEATURES
<ul>
<li>Disable Pagination in nav menu add item lists </li>
<li>Preserve hierarchy in category nav menu add item list and posts category selector</li>
<li>Automatically scroll to first checked item in post category selector </li>
<li>Preserve WooCommerce category hierarchy</li>
</ul>

Preserve Taxonomy Hierarchy

Preserve hierarchy in posts category and navigation menu editor lists.

Network Sites Hierarchy vs Preserve Taxonomy Hierarchy