Boston Legal consistently presented LGBTQ+ characters with dignity and agency, notably through Clarence Bell's arc and numerous legal cases championing queer rights. The show's narrative stance was largely affirming, portraying prejudice as an external societal issue rather than an inherent aspect of queer identity, resulting in a net positive impact.

Boston Legal features a significant storyline where a transsexual character is depicted as a victim of workplace discrimination. The show's narrative, through its protagonist Alan Shore, strongly advocates for her rights and dignity, framing prejudice as an external injustice. The legal victory reinforces a positive and affirming stance towards transsexual identity.

The show frequently satirizes or critiques conservative Christian viewpoints and adherents, often portraying them as hypocritical, irrational, or bigoted, particularly in cases involving social issues. While defending religious freedom, the narrative often positions the audience to view these specific expressions of faith as problematic.

When Islam or its adherents are depicted, it is often in the context of discrimination or prejudice, particularly post-9/11. The narrative consistently condemns such bigotry, positioning the audience to sympathize with and defend Muslim characters.

Through the character of Alan Shore, a central protagonist, Judaism is portrayed as a respected aspect of identity. The show does not satirize or criticize Judaism itself, and any instances of anti-Semitism are condemned by the narrative.