ognjen.kuljic

Some very useful plugins like Regenerate Thumbnails leaves old files behind, so it is good practice to clean after it.
Features: 
*Remove all unused files from upload dir (Unattached files to posts or pages), 
*Remove all leftover files (forgotten files in upload dir).

qCleanup

This plugin allows you to delete unused and leftover files from upload dir. In one click you can rid of all unwanted files and reduce space usage.

neoslab

Database Toolset can help you to keep your database clean and optimized by deleting all orphaned or unneeded entries such as “transient”, “revision”, “auto draft”, “orphan postmeta” and much more.
Furthermore Database Toolset can be used to optimize your database using the native SQL function in order to increase your website performance and can also be used to organize scheduled database backup which will be saved on your website root.
Major features in Database Toolset include:
<ul>
<li>Remove “revision”, “draft”, “auto draft” from your database.</li>
<li>Remove “moderated comments”, “spam comments”, “trash comments” from your database.</li>
<li>Remove “orphan postmeta”, “orphan commentmeta”, “orphan relationships” and “dashboard transient feed” from your database.</li>
<li>Allow user to perform an “Optimization Process” of his database using native SQL function.</li>
<li>Allow user to configure an automatic backup of the database which will be save in the website root.</li>
</ul>
<h3>License</h3>
Good news, this plugin is free for everyone! Since it’s released under the GPL, you can use it free of charge on your personal or commercial site.

Database Toolset

This extension is really very simple configuration

Great and simple

Database Toolset can help you to keep your database clean by deleting all unneeded entries such as "transient", "revision", "auto draft" and more.

qCleanup vs Database Toolset