As a comic book collector, the continuity for the classic minicomics has also been of interest to me and last week I finally decided to sit down and work out a reading order for the series. I based this first on the order in which people/vehicles/powers are introduced and reused, and secondly on what made a good overall 'flow.' Since the comics sort of run in 'seasons' like TV, I liked to build to a big battle at the end of each wave of books.
NOTE: I do own quite a few of the whole run, but do to my research I used the totally awesome site The Good Old Days, which I highly recommend as the most thorough collection of He-Man and She-Ra reading I have seen anywhere on the 'net. It's all too low-res to reprint, but for pure reading and completist enjoyment it can't be beat: http://www.goodolddays.net/comics/index.pl?id=22
Anyway, after the first four books ("Power Sword," Battle in the Clouds," etc) which I think are numbered 1-4 and run as such, you have the 2nd series (i.e. "He-Man Meets Ram-Man," "Teela of Teela") which basically run in the order in which the Heroic and Evil Warriors amass their allies. All you need to do is see who's working for He-Man and Skeletor in each issue, and the order becomes clear.
The Magic Stealer
Ordeal of Man-E-Faces
He-Man Meets Ram Man
The Terror of Tri-Klops
The Menace of Trap Jaw
The Tale of Teela
The Power of Point Dread!
The last two books are interesting because they're actually Part 1 and 2 of the same story, in which Skeletor tries and fails and tries again to gain control of Point Dread. It's the only two-parter in the whole series, really.
I'm gonna break this up, so next post: Horde! Snake Men! Eternia!