Hi!
I've just joined the forum and a very newly Boxster owner (2004 Boxster S) having purchased one a couple of weeks ago.
Just thought I'd post this here as it may be some help - I put together a checklist when I was researching from various sources and looking at various cars and hopefully, it will give you something to go through when you compare the dealer car and the cheaper local one.
Maintenance costs are in £GBP as I'm in UK.
It really helped me as I was stung with a first purchase that ended up having to be returned to the dealer due to a major fault. The latest one just passed its post-purchase inspection with flying colours PHEW! 
986 Checklist
Service Schedule
 Every 5,000 miles  Oil and filter change (as recently recommended by experts)
 12,000  engine oil and cabin filter (minor)
 24,000  Engine oil and filter, cabin filter, air filter (major)
 36,000  Minor
 48,000  Major + fuel filter + serpentine belt, brake discs, clutch, ignition coils, IMS bearing, rear main seal, coolant
 96,000  48k + Fuel filter, serpentine belt, transmission fluid, transmission filter, suspension arms/bushes, shocks, oil air separator
 Every 2 years  Brake fluid
 Every 4 years - Spark Plugs
NOT ALL OF THESE ITEMS WILL NEED REPLACING - SOME JUST CHECKING
Garage Maintenance Costs
 Fuel filter - £150
 Serpentine belt - £150
 Spark plugs - £150
 Coolant - £250
 Brake discs - £600
 Igniition coils - £500
 Clutch, IMS and RMS - £1,400
 Tyres - £500
 Oil air seperator - £200
 Water pump - £300
 Alternator - £500
 Transmission fluid and filter - £300
 Suspension arms/bushes - £900
 Shocks (4) - £1,500
 Differential fluid (automatic) - £250
Checklist
Exterior visual check
 Walk around the car and check for rust, damage, etc.
 Headlights  check for cracks, brown or burning spots
 Front bumber  no cracks or damage or discolouration
 Tyres  Check for cracks, tread and age
 Wheels  check for excessive damage
 Sides  Check for damage, discolouration and check panel gaps
 Rear bumper- Check for cracks, damage or discolouration
 Tailights  Check for cracks or damage
 Third brake light  check for cracks or damage
 Rear  check for panel gaps and ensure they are even
 Front windscreen  check for cracks, large chips
 Knock on exhaust and check sound
 Check suspension springs for corrosion and damage
 Check brake discs and pads
 Check callipers
Interior
 Check door panels  no delamination or pulling away. Check door handles and storage boxes work
 Check seats to ensure no major rips
 Check behind seats for damage
 Check carpet behind seats for damage and dampness
 Check for missing headrest filters
 Check for missing centre wind deflector
 Pull up carpet behind seats and check for dampness
 Check lights  ensure they all come on in keys first position
 Check oil level to ensure between min and max and not overfull
 If warm  check passenger side fan comes on
 Check hazard lights
 Check radio works with all speakers (including rear speakers if present)
 Check climate control or air con works
 Check front radiator fans are working  both sides and one in middle for S model
(run hand under bumper)
 Check radiators by front bumper  check for debris and for any rust or leaks
 Check windows open and close with no excessive creaking or delay
 Check windows open and close automatically when opening doors
 Check handbrake for excessive play or noises
 Check heated seats work if present
 Check glovebox if present
 Check front carpets
 Rear plastic window check for cloudiness and marks (if plastic)
 Start engine and check for smooth starting and no subaru sound or jumping or
knocking or tapping
 Check mirrors adjust
 Check seats electronically adjust
 Check seats slide forward and back
 Check wipers and washer fluid
 Check obc (on board computer) (if present)
 Check indicators
 Check headlights
 Check brake lights
 Check cup holders (if present)
 Check both trunk buttons work
 Check rear spoiler button works
Trunks
 FRONT
o Check front struts
o Check spare wheel
o Check brake fluid
o Check battery
o See if hood sticker is correct and check paint matches bumpers o Check tool kit 
  REAR
o Check rear boot struts
o Check coolant tank level (if bottle is bright white probably been replaced recently)
o Check boot carpet for dampness and check bottle for cracks o Check under oil cap and coolant cap for mayo type substance
Roof
 Lower roof and raise roof twice
 Check for smooth motion
 Check roof sits flush when open and closed  no warning lights
 Listen for loud popping noise when raising and lowering room
 Check for rips, tears or damage (small amount of mold is common)
Engine Bay
 Check engine bay for missing covers/carpet
 Check drainage channels are clear and dry
Test Drive
 Wait until up to 80 degrees Celsius before going over 3.5k revs
 Listen for creaking and clonking in suspension during test drive
 Acceleration should be prompt
 Gearbox should be light and gear changes smooth
 Clutch should be lightish
OBD Test
 Diagnostic codes
 History
 Check emissions
 Check voltage
Paperwork Check
 Service history should be fairly thorough for a well looked after car
 Water pumps, clutches, exhausts, intermediate shaft, IMS, flywheels, etc. are all
common parts to replace in 986s
 History of recent IMS replacement is a bonus but not mandatory