OPINIONS: The Mishnah states that the testimony of a witness about the identity of a corpse is not acceptable unless he recognizes the forehead and nose of the dead person.
RABEINU TAM in SEFER HA'YASHAR (#92, cited by TOSFOS DH Ein and other Rishonim here) asserts that it is not reasonable to suggest that a dead person can be recognized only through his facial features. If the witness is familiar with the dead person's bodily features, he certainly may identify the corpse based on those features. Rabeinu Tam explains that the Mishnah's law refers specifically to a head without a body. A witness who saw the head of a dead person (detached from the body) may identify it only if he recognized the forehead and the nose. If, however, the rest of body was present and the witness recognized its bodily features, his identification of the dead person certainly is acceptable.
The RASHBA and other Rishonim (121a) reject Rabeinu Tam's explanation. They argue that the Mishnah makes no mention of the body, implying that regardless of whether or not the body is present the witness may identify the corpse based only on recognition of the forehead and nose.
The ARUCH LA'NER resolves this and other questions which the Rishonim ask on Rabeinu Tam's explanation. He points out that the Rishonim did not have the original version of Rabeinu Tam's Teshuvah as it appears in the Sefer ha'Yashar; their questions on his explanation is based on the brief excerpt of his words as cited by Tosfos. In the original Teshuvah, Rabeinu Tam clearly explains that the Mishnah discusses one whose testimony is based only on "Simanim," specific features, and who does not have "Tevi'us Ayin," general recognition, of the corpse. Accordingly, the Mishnah states that one must recognize the forehead and the nose because "Simanim" are a valid form of identification only when they appear on the head (forehead and nose), whether or not the head is attached to a body. Only when one testifies about the identity of the corpse based on "Tevi'us Ayin" (general familiarity) may he testify based on recognition of the rest of the body. The Mishnah discusses recognition based on specific signs ("Simanim"), and thus it refers only to testimony about the specific features of the head.
HALACHAH: The SHULCHAN ARUCH (EH 17:25) cites the opinion of Rabeinu Tam and writes that other Rishonim disagree.
However, when one recognizes the body or head through "Simanim Muvhakim" -- clear signs unique to this person, his testimony is accepted. "Simanim Muvhakim" are always accepted mid'Oraisa as testimony, regardless of whether one maintains that testimony based on ordinary "Simanim" is accepted mid'Oraisa or mid'Rabanan.
The RAMBAM (Hilchos Nachalos 7:3) writes that if a person was killed and witnesses did not recognize the face but testified about "Simanim Muvhakim" they found on his body, Beis Din may not permit his wife to remarry. The Rambam seems to rule that even "Simanim Muvhakim" are not accepted as testimony. This also seems to be the ruling of the SEFER HA'ITUR (as cited by the BEIS YOSEF).
The BEIS YOSEF (EH 17:40, and KESEF MISHNEH, Hilchos Gerushin 13:21) asks that the Gemara here contradicts the ruling of the Rambam because it implies that even if ordinary "Simanim" are mid'Rabanan, a mole which is a "Siman Muvhak" certainly is accepted as testimony mid'Oraisa. Moreover, the Rambam himself (Hilchos Gezeilah 13:5) writes that "Simanim Muvhakim" are accepted for all testimony mid'Oraisa, and, in accordance with this principle, he rules (Hilchos Gerushin 3:11) that one may return a Get based on a "Siman Muvhak" (such as a hole next to a certain letter).
The Kesef Mishneh therefore concludes that when the Rambam in Hilchos Nachalos writes that a "Siman Muvhak" is not accepted, he refers to what the Gemara here calls an ordinary "Siman" and not an actual "Siman Muvhak." A "Siman Muvhak" which is acceptable, even according to the Rambam, is a "Siman" which is very unique and singular to this person. Everyone agrees that testimony about such a "Siman Muvhak" is acceptable. The Kesef Mishneh concludes that this must be the intention of the Sefer ha'Itur as well.