Here is a list of tools that allow you to document your databases.

Database Note Taker

Database Note Taker is free, making it easy to capture and share knowledge about your databases and simplify database documentation. It provides developers, support staff and even customers with quick and easy access to documentation.

Commercial: Free

Free edition: Yes

Allows editing: Yes

Metadata stored in: External repository

Export: HTML

ER Diagram: No

Dependencies: No

ApexSQL Doc

ApexSQL Doc tool is a SQL database documentation tool that enables documenting SQL Server databases. It automates and schedules documentation unattended and provides fully customize documentation output.

Commercial: Commercial

Free edition: Yes

Allows editing: Yes

Metadata stored in: External repository

Export: CHM,HTML,MS Word,PDF

ER Diagram: No

Dependencies: Yes

MySQL Workbench

MySQL Workbench is a visual tool for database architects, developers and DBAs. MySQL Workbench provides data modeling, development, administration and documentation tools for MySQL.

Commercial: Commercial

Free edition: No

Allows editing: Yes

Metadata stored in: Database comments/extended properties

Export: HTML

ER Diagram: Yes

Dependencies: Yes

dbForge Documenter for MySQL

dbForge Documenter for MySQL is a handy MySQL and MariaDB documentation tool that automatically generates documentation of an entire MySQL database in HTML, PDF, and MARKDOWN file formats. The tool allows users to customize the generated documentation up to their needs with the help of a bunch of options and settings.

Commercial: Commercial

Free edition: No

Allows editing: No

Metadata stored in: Database comments/extended properties

Export: HTML, PDF

ER Diagram: No

Dependencies: Yes

More Database Documentation Tools you can find here: