Definition
Unity offers two ways to execute managed code. Mono ships the assemblies and compiles them at runtime. IL2CPP converts them to C++ during the build and ships a native binary. You pick one per platform in Player Settings under Configuration. Some platforms only support IL2CPP, so the choice is not always yours.
Relevance
This one setting changes what the player contains and how long the build takes. Mono ships the assemblies and is quick to build. IL2CPP spends the build generating C++ and ships a native binary. Platforms such as iOS and WebGL only offer IL2CPP.
Example
A team ships Windows with Mono for quick builds and Android with IL2CPP. The Windows player has a Managed folder of assemblies. The Android player has a native library plus global-metadata.dat. Same scripts, two different ways of running them.