your question covers a wide range as there is a distinct difference in approach that mustang owners take if they favor a classic (60's/70's) vs others that like the newer profiles.
it really becomes a personal preference and sometimes also one of practicality, ie whether the car will be used regularly or kept in the garage for a lot of the time.
for me the best mustang is 03 or 04 cobras (terminator series).
these were among the most special mustangs built and were very limited production:
in 2003 ford produced only 13,400 cobras, of which 5082 were
in 04 only 5664 cobras were produced , of which only 1896 were
the engines were hand assembled using race ready (forged) internals within a stock 4.6 block. the cobra came stock with performance cold air intake and a medium boost supercharger aluminum heads and performance equipment. The engine was rated at 390hp
they had other things rarely if ever seen on a mustang (not a complete list):
-short throw 6 speed transmission
-brembo discs on the front, oversize on the rear
-independent rear suspension
-custom seats (leather & suede with cobra insignia)
they are very fast (stock times were in the order of 4.5 seconds 0-60, and 1/4 in less than 13.
the engines because of high quality internals are exceptionally dependable, therefore whether goal is long term durability, or performance upgrade a cobra engine is 1 of the best places to start.
this is my 3rd mustang convertible, 1st was 68 with optional 390c.i. engine, 2nd was heavily modified 01 gt convertible.
here's my 04 cobra