Lemme see what I can remember, from what I've read.
I know they changed optional interior & exterior colors a few times over the years.
For '87-90:
On the 2.3L, steel wheels with hubcaps were standard, Polycasts were optional, and 10-holes were also optional (I think). On the 5.0, 10-holes were the only thing available. In '90, Mustangs got an airbag so the steering column and wheel changed and the tilt column disappeared. As 351Wcoupe said, somewhere in there (I think after '87 or '88) they changed the climate controls, the early ones had a panel with 3 round openings which the controls were in, later ones just had one large oval opening and the controls are different. Some '89s have the 25th anniversary emblem on the dash, some don't...just as some '90s do and some don't. Also at some point in here 5.0 LX's started having GT seats as an option of some sort.
'91-93:
All LX's got body colored side moldings. I believe the wheel choices for the 2.3L stayed the same. On the 5.0's I believe Ponies were standard if you got the handling package, otherwise they still had 10-holes. Front fender openings were larger to accomodate the 16" Pony wheels. Can't think of anything else right now.
There are a few things I'm unsure of, for example some cars came with the center console armrest delete (like mine) but some still had the armrest. I think I heard that anniversary models had the delete

Dunno.
Also, I've seen door panels without map pockets. I'd like to know how that came about because I don't know how you could option off map pockets. Additionally, I've seen door panels where the trim above the arm rest (the piece that has the same material on it as the seats) was covered with vinyl (were there cars that came with vinyl seats?), and I've even seen door panels that did not have that trim piece there at all, and it was factory. Anybody know about that?