Dirty lil' secrets, huh? I bought my '06 GT two and a half years ago @ 73k miles. Drove nicely, paint was in good shape save for a few chips and a small dent. Engine bay was clean. Didn't seem to have any issues, no codes stored, etc. Though I instantly recognized the guy had a rather extreme short throw hiding underneath the boot as soon as I went into 1st. Poor red leather seats, the front driver's seat was completely ripped up and dried out, so I knew the car had been abused. Fuckin' fatass didn't bother to care for them.
I expected there to be things I would need to fix, but not to the extent that I ended up fixing it. Basically, the car's entire suspension ended up being at the end of its life (all control arm bushings quickly reached end of life, struts gave out), the clutch started giving out, and problems began mounting (hesitation under load, overheating, bad alternator/open diode issue, melted electric relay, radiator corroded inside, sparks shot, lash adjusters loose and knocking). I'm not one to let things fester, and working at a certain, very large Mustang parts supplier, I do this stuff every day. The result is a "rebuild it/fix it" list to get my '06 looking and running better at 121k miles than it did at 73k miles.
FRPP Rear Lower Control Arms
FRPP Front Lower Control Arms
Flowmaster Outlaw Axlebacks
PA Performance 180A Alternator
PA Performance Power Wire Kit
Exedy Stage 1 Clutch Kit
GT500 Front Strut Mounts
ST Sport Front Struts
FRPP Performance Spark Plugs
OEM Rear Rotors + Pads
OEM Front Rotors + Pads
2nd Exedy Stage 1 Clutch Kit (first clutch job from shop I'll never go to again was shit, clearances all jacked up)
FRPP Rocker Arm + Lash Kit
FRPP Blue Valve Covers
Mishimotor Performance Radiator
SVT Cobra Electric Radiator Fan
Ford OEM fuel filter
Ford OEM MAF sensor
New Air Intake/Filter
(2) Front and (2) Rear O2 Sensors
New Springs Front/Rear
New Rear Bumper Cover Painted
TL;DR: If you buy a Mustang, be prepared to fix things on it. It's an economy sports car that young and ignorant folk can buy and thrash on.