Many companies (especially smaller ones) feel they do not have the work force or time to deal with properly implementing signed TLS certificates across their organization. This can lead to potentially serious problem because of the user’s perception while browsing the company intranet sites. If something potentially is hacked and everyone is accustomed to clicking through certificate warnings, then company accounts and data can easily be compromised.
Organizations that deploy Microsoft Certificate Services or even their own Certificate Authority (CA) using the OpenSSL toolkit are in a much better position to handle attacks and organize their application infrastructure.
Think twice about clicking through Pop-ups. What is the cost of a breech? Get a recognized root CA deployed to your clients and install the associated server certificates on all of your user facing systems.