The content (attribute value) of the eduPersonTargetedID attribute is defined to be a SAML 2.0 persistent NameID (cf. MACE-Dir SAML Attribute Profiles, section 3.3.1.1, lines 390-393), i.e., an XML structure. Abstractly it's a 3-tuple made up of the IDP's entityID, the SP's entityID and the subject-specific part. It could be called a "service-specific pseudonym" in that it's an opaque identifier that differs for each service a subject is accessing.

Deprecation

The eduPersonTargetedID SAML Attribute has officially been deprecated. No new deployments should be making use of this attribute and any existing deployments should make plans to migrate to the SAML pairwise-id attribute. The new replacement attribute is simpler and therefore preferable in all regards: It's a simple attribute with simple string values (instead of a complex XML data structure), it has a single, consistent way of requirements signalling from the Service Provider and a single, consistent on-the-wire representation. It is also defined in an official OASIS SAML 2.0 Profile, not merely part of a community "standard" (eduPerson), and not specific to edu-anything. So transitioning to the pairwise-id SAML attribute should be started ASAP.

This deprecation should come as no surprise to anyone as the eduPersonTargetedID SAML Attribute – as container for persistent NameIDs – was essentially obsoleted in 2005 when SAML 2.0 defined a standard method to send this same data structure in the Subject element of the SAML Assertion.

Issues

• All forms of eduPersonTargetedID attribute as well as all forms of the SAML 2.0 persistent NameID itself suffer from a case folding issue (when using base64 encoding) that may lead to identifier collisions at Service Providers not treating identifiers as case-sensitive. Consider this an informal Security Advisory against any use of this attribute (or persistent NameIDs in general).
• saml2int – the Interoperable SAML 2.0 Deployment Profile, a normative part of eduID.at via the SAML WebSSO Technology Profile – states in Version 0.2 that persistent NameIDs should be transmitted in the Subject of the SAML Assertion, not as an eduPersonTargetedID Attribute (value). So use of eduPersonTargetedID within eduID.at actually constitutes a formal policy violation.
• Also note that the new version of saml2int goes much further and states that:

SPs MAY support legacy or historical <saml:NameID> and <saml:Attribute> identifier content for compatibility reasons but MUST NOT require their use.