List Entries in a section that are referenced as a relation in another
You could use the without filter for this:

{% set entryParams = {
    section: mySection1
} %}

{% set relationParams = {
    sourceElement: mySection2,
    field: myEntriesField
} %}

{% set entriesWithRelation = craft.entries(params).relatedTo(relationParams).find() %}
{% set entriesWithoutRelation = craft.entries(params)|without(entriesWithRelation) %}