Definition
Unity compiles scripts in the Assets folder into a few predefined assemblies. Assembly-CSharp.dll holds your regular runtime scripts and is compiled last, so it can reference everything else. Scripts in the special Plugins and Standard Assets folders compile earlier into Assembly-CSharp-firstpass.dll. Assembly definition files let you split code into your own named assemblies instead. In a Mono build these DLLs sit in the Managed folder of the player.
Relevance
Assembly-CSharp is the default home for gameplay scripts. Anything in Assets that no assembly definition claims ends up here, compiled last so it can reference plugins, packages, and the engine.
Example
A player health script, a shop controller, and a login client all live in Assets without assembly definitions. The build compiles all three into one Assembly-CSharp.dll.