Linking involves packaging together all of the .obj files built from your source files, as well as any .lib files you reference, into your output (eg .exe or .dll).
Without incremental linking, this has to be done from scratch each time.
Incremental linking links your exe/dll in a way which makes it easier for the linker to update the existing exe/dll when you make a small change and re-compile.
So, incremental linking just makes it faster to compile and link your project.
The only runtime effect it might have is that it may make your exe/dll slightly bigger and slower, as decribed here:
http://msdn.microsoft.com/en-us/library/4khtbfyf.aspx
Edit: As mentioned by Logan, incremental linking is also incompatible with link time code generation – therefore losing a possible performance optimization.
You may want to use incremental linking for debug builds to speed development, but disable it for release builds to improve runtime performance.
Delay loaded DLLs may be what you are thinking of: