I don't blame him for having other things to do, but I haven't gotten word back from him yet so I thought, rather than wait an unpredictable amount of time, that I would let you guys look.
The first comes from Pathways into Darkness, alluding to The Hobbit. Quoting the description given of the Alien Pipes,
This bizarre musical instrument reminds you vaguely of a book you once read while you were a child. You can't quite place it.
Now, remember that is was described by the first dead German you encounter as being covered in green cloth. Compare that with this line from The Hobbit:
(...) They came back with viols as big as themselves, and with Thorin's harp wrapped in a green cloth. It was a beautiful golden harp, and when Thorin struck it the music began all at once (...)
As for the location of the passage, it is found in the chapter An Unexpected Party just before the Dwarves begin their song. Sorry my good copy of The Hobbit is not available to me now, so I can't give page numbers, but then who needs to know that?
Anyway, it seems to me that You in PiD (I shall avoid using his name Sgt. Eddings) would've been able to remember The Hobbit from Your childhood, seeing as how The Hobbit was first published in 1936 and intended as a children's book.
The second is from Marathon Infinity, alluding to The Lord of the Rings, The Return of The King. Again, my good copy which kept separate page numberings is not available to me, so I instead must only cite down to the chapter number.
Volume III, book 5, chapter VII (7!) "The Pyre of Denethor", about the middle of the chapter. With the huge paperback released for the three movies, it is on page 836.
Then Denethor leaped upon the table, and standing there wreathed in fire and smoke he took up the staff of his stewardship that lay at his feet and broke it on his knee. Casting the pieces into the blaze he bowed and laid himself on the table, clasping the palantír with both hands upon his breast. And it was said that ever after, if any man looked in that Stone, unless he had a great strength of will to turn it to other purpose, he saw only two aged hands withering in flame.
If you don't mind Hamish, perhaps you have other copies that you could use to refer the page number?
This allusion is not the same, not so definite I think, as the previous one. To understand it, you have to recall the 'motif' of the bloody hands in Mi. They occur in the Prologue chapter screen and the final screen.
Here's and anecdotal story of why I'm sending this perceived allusion to you. Well, before I knew much about The Lord of the Rings, I noticed those bloody hands in Mi. A few years later, I listened to a BBC dramatization of TLotR -- recommended to any interested -- and noted the passage about Denethor's hands in the palantír. I immediately thought of Mi. Obtaining that paperback copy of TLotR which I cited from, I realized that the mention of Denethor's hands was not added in the dramatization.
Considering that especially Mi draws other influences from Tolkien, I find it likely that this is not just the product of my imagination.
As for any importance with this allusion, it doesn't necessarily add to the understanding of the Marathon Story. So I send this merely because Marathon Story aficionados enjoy allusions so much (I should know).