Running Minecraft with your own mods on a headless server can be super nice.
This allows you to add some quality-of-life mods.
Installation
First of all, make sure to complete the setup of the vanilla Minecraft server and start the server at least once. 
You can also do this installation on any existing Minecraft server.
However, make a backup first, just to be sure!
- Download the Forge Installer to your `$GAME_DIR. Make sure to pick the installer for your Minecraft version.
 - Run the installer with 
java -jar forge-*-installer.jar --installServer. This will install everything. 
Get Mods
Forge is now installed and you can add your mods.
- Create the 
$GAME_DIR/modsfolder. - Download all of your mods. Be careful that the mod is for the correct minecraft version. Some mods also come with support for another mod loader. Be sure to pick the Forge version.
 - Copy those mod files into the 
$GAME_DIR/modsfolder. 
Start the Server
Just call the forge-$version.jar as if you would call the original Minecraft server jar.
java -Xmx1024M -Xms4096M -jar minecraft_server.*.jar nogui
How To Install Mods
- Download the mod's 
*.jarfile. - Copy the 
*.jarfile to the$GAME_DIR/mods/directory 
List of Useful (Server-Side only) Mods
- FallingTree Instant Tree feller.
 - GravelMiner Instant Gravel mining.