I know 99-04 cars usually get lumped into the same category.....but this thread is dedicated the "little things" that differentiate the different years from each other.
Good OPs go first:
Sometime in 03, they changed the design of the interior A-pillar Trim. I think the reason was for safety reasons. The pre-03 cars had a skinnier design, the later models had a "fatter" design.
2001 Bullitts & 2003/2004 Mach 1's had a different C-pillar exterior panel. The design on the bullitts/machs "swept forward" flowing with the body lines of the side scoops while GTs/V6s/Cobras had the standard C-pillar that kinda curved downward. The outside panel, inside panel, and even the glass were different on these cars vs. the Gts/v6s/Cobras.
Interior Cargo Net:
2002-2003 non-convertible models had an interior cargo net on the roof liner. (I need clarification on this. I'm pretty sure it didn't come on 04s, but did it come on ALL 03s and some 02s?)
Your turn, GO!