Salt Lake Temple
The Holy of Holies is one of the least talked about rooms in the temple. This is because, as the name suggests, it is a temple's most sacred room. There is much we don't know about the Holy of Holies and some of what I say in this post will be speculation.
The Salt Lake Temple Holy of Holies as it appeared in 1911
The Salt Lake Temple includes a special room designated as the Holy of Holies. Salt Lake is the only temple that has this room. The Salt Lake Holy of Holies is adjacent to the Celestial room, between the two original sealing rooms. It has a stained glass window that depicts the first vision and a domed ceiling that projects into the floor above. It is used by the prophet when he needs special guidance (The House of the Lord Pg. 192-194). The back side of the stained glass window can be seen from a seldom used hallway that runs behind it and the sealing rooms.
It appears that designating a room of the temple as a Holy of Holies began with the earliest temples built by the modern Church. While the Kirtland Temple did not have a specific room set aside as a Holy of Holies; Scott (who writes The Trumpet Stone blog) has pointed to Doctrine and Covenants 110 in his post on the Holy of Holies where he suggests that, because Christ and ancient prophets appeared there, the second floor east pulpits could be considered the Holy of Holies for that temple. The original Nauvoo Temple had a sealing room in the attic adjacent to the Celestial Room that served as a Holy of Holies (The Sacred Departments for Temple Work in Nauvoo pg 8). My speculation is that for the Logan Utah Temple it used to be the "Gold Room" (which since the 1977 rebuild no longer exists). The "Gold Room" was an extremely ornate sealing room with gold leaf adhered to the walls in intricate patterns almost like gold wallpaper. I also believe that for the Manti Utah Temple it is the "Wells Room," a no longer used sealing rooms adjacent to the Celestial Room, which is also elaborately decorated and has a half domed ceiling above the altar.
Fort Collins Colorado Temple
Similar to the rooms described above most every temple has a sealing room that can function as a Holy of Holies if the prophet needs one (ldsliving: What the Church Has Said About the Holy of Holies). It appears, and some other people who blog about temples have speculated, that in most of the temples one sealing room has a small closet with the items needed (most noticeably a sink) for the administration of the sacrament and that this is the sealing room that can function as a Holy of Holies. Please note that this is speculation! The Sealing Room in the extreme upper left corner of this floor plan of the Ft. Collins Colorado Temple has such a closet as does the Sealing Room to the far left (labeled Instruction Room #1) of this floor plan of the Philadelphia Pennsylvania Temple. Note that in both cases chairs are set up in front of the closet door, showing that the closet is not meant to be used routinely.
President Lorenzo Snow
In the September 1933 issue of the Improvement Era in an article entitled "An Experience of my Father's" LeRoi C. Snow tells of President Lorenzo Snow's experiences in the Holy of Holies of the Salt Lake Temple just before and after the death of President Wilford Woodruff. While this story has been retold several times the original goes into much greater detail than the latter retellings. Of particular interest to me is the fact that this strongly suggests that the Holy of Holies is not just open to the President of the Church but to the President of the Twelve also, and possibly others.
When President Spencer W. Kimball was seeking guidance leading up to the announcement that all worthy men could hold the priesthood he spent a great deal of time in the Salt Lake Temple, including long into the night. He apparently knelt in prayer in several different rooms, and occasionally was accidently interrupted by temple workers who didn't know he was there. He also prayed in the Holy of Holies (Priesthood Restoration and Spencer W. Kimball and the Revelation on Priesthood).
President Nelson during the April 2018 General Conference
President Nelson, in his talk “Revelation for the Church, Revelation for Our Lives” in the April 2018 General Conference discussed how he chose his counselors in the First Presidency. He said that after meeting with each of the Twelve: “I then sequestered myself in a private room in the temple and sought the Lord’s will.” This private room could possibly be the Holy of Holies.