I’m a self confessed BMW and Porsche nut and although I have a 996 C4S that I bought with my dad as a project with not far off 80k. My 987 Boxster S had bore score... and was a pretty bad experience.
My 996 I bought it from a reputable dealer (strasse Leeds) and have had a very good relationship with them for 10 odd years and has looked after all mine and dads porsches so felt much more confident as it had a PPI and lots of work done.
I sold my Z4M coupe to go travelling and then bought a 2005 3.2 boxster S about 2 years later to get back into a sports car. I always wanted a 996 C4S but at the time I couldn't afford one and my thinking was... in terms of paranoir as the 2.7 and 3.2 have the smallest chance having issues as they are the smallest bore. (Plus they are cheap...)
It was lovely full spec, extended leather, Chrono, Bose, 72k full Porsche service history had it 2 weeks did 1000 miles and it started knocking, took it to strasse hoping it was nothing serious as they can get sticky tappets which does sound very similar and the noise comes from the drivers side air vent if there is an issue. After an inspection they found the RMS was leaking, the IMS you might as well do at the same time. The gear shift wasn't quite right and sometimes if the RMS has been leaking for a while it can get to through to the clutch friction plate making it slip so clutch was a gonner to... at that mileage and because everything needed to come out might as well do the flywheel. Put the borescope down and was found to have bore score and the bits I knew about... ac rads needed doing (they only really last 6 years if your lucky with the way they are set up as a stone can puncture them) needed disks and pads all round they often look fine but corrode on the inside, the rear light had a crack and a couple of other odds and sods like the air vents are renowned for breaking and 2 were broken same with the fan and temp control buttons and you would be amazed at the cost to repair
Cost to repair was quoted as £11500 and I paid £11750. After some really good advice I thankfully I managed to get my money back due to UK consumer law with the car not being fit for purpose. Drove it from Manc to Leeds then had to limp it to Birmingham to hand back. Big lesson learned GET A PPI before you buy all this stuff you can't see and it won't rear its head until its too late.
Something to bare in mine while looking you will find cars with similar mileages and years with quite varying prices, they are reliable cars but like any old sports car once the bits start adding up you can be in the whole quickly. Just disks pads, service and say the AC rads and hoses could rack up a 3-4K bill when the cars aren't that expensive. This is the reason, there were loads made and many didn’t look after them like they needed too. The 986/7 generation shared 90% of the parts with their bigger brother so are similar money to look after yet if you go on any 911 forum they are so anal about servicing etc but 987s weren't seen in the same regard by many owners. Especially once they got down to 10-15k service history can be a bit all over the place.
Again the Z4 3.0 and the Z4M are in completely different brackets in terms of cost of ownership. The 3.0 offers probably 85% the car for 50% ownership cost so can't really be directly compared.
The 2.7 and 3.4 987s aren’t, as I said they have 90% the components of a 911 and the engines are all similar units just with a bigger bore. So pricing to look after is similar.
On the other hand in the last 10 years we’ve had 996 997 and a 991 and tbh its cost me more to service and look after the Z4M from my experience. Thats not to say if anything did happen it wouldn't be a lot but having a good relationship with an independent is worth its weight in gold.
The biggest bill on the 997.1 was the radiator hoses and AC condensers as the sub frame need to come out but even so think that was £1200. Servicing is a little cheaper than the M generally but as these cars were 80-100k the parts can be expensive, but with the 996 sourcing fabulous second hand parts isn't difficult these days. They haven’t been crazy money to look after outside service schedule.
The 996 4S had everything done before I bought it by the previous owner and I've mainly done cosmetic bits. Everything including tyres, servicing and issues including IMS, RMS, clutch, flywheel, radiators, hoses, MOTs etc the paper work adds up to about 15k over the 16 year life. About £1000 a year which isn’t horrendous but it has had lots of premature work done to keep it in good nick.
It hasn’t put me off I’m planning on my next car to be a 997.2 4S but that has less issues.
The thing to do is to go in eyes wide open don’t assume it will be fine because as in my case the car was a scrapper but thankfully because I bought it in the dealer network I had a safety net. If it was private... different story and I learner my lesson. I didn't believe the internet and I still think you have to be unlucky but it can happen.
Couple of observations on comparing the cars in question. I almost bought a 987 Cayman S before my Z4MR but it depends what type of guy you are. I like my cars a little bit more on the edge and the boxster and caymans are just fabulous, meaning they are really good, make you feel like a god driving them. Point it to an apex that's where it goes, but it’s so hard to step them out and have a bit of fun. I found them a bit sterile... but purposeful you can make ground very quickly in them but just a bit lacking. They also make power far further up the rev range compared to the S54 in the M, they make 80% of torque at 2500 rpm and get going quick but the 987s are more like 4.5k so you need to ring them a bit more to get the feel, driving around town they can feel quite slow and they drink fuel like no tomorrow, the Z4M I find is pretty good for its output and the 3.0SI is even better you could hit 40mpg on the motorway with it...
The Z4M in comparison feels like an axe murderer and wants to put you through a hedge backward on a damp road. Stepping it out is litteraly a flick of the throttle. It’s also harder to drive quickly on A and B roads you have to grab it by the scruff of the neck. I think because the Z4M was my first sportcar and they have quite a bit more power they 987 felt a bit underwhelming for me. The Z4 also feels a bit more modern the 996/7 were the first modern cars Porsches and the interiors and tech haven’t aged all that well IMO although you can put double din entertainment systems in with airplay etc.
The 987.2 was made is low numbers so finding one in a decent spec is difficult but they improved with a much more reliable engine but they seem to be held at a premium because of this. The 981 generation fixed pretty much all these issues by giving it more power and also has the upgraded unit with very few issues. That would be my starting point if i was looking and the unlike the 2.7 in the 987 the 2.7 in the 981 is similar on the road to the old 3.4 S and is a much nicer place to be.
The 911s are a completely different proposition the 997 is probably my fav simply because in the newer generations they feel a bit heavier less direct with electronic steering and the engine has creeped further and further forward over the years that they aren’t far off being mid engined in the 992.
The newer ones also have a few to many electronics. But for pace and as a GT the 991 is a fabulous car it was a great car to take across Europe but I just felt the 997 was a better drivers car in my previous eurotrip. They just have the best between old and new and although flawed the 997.1 3.8 with sports exhaust sounds epic. The newer DFI engines don’t sound as good IMO.
The 997 is a bit more on edge and you know the engine is out the back and feels like a Z4M in the axe murdering department but the 911s just feel superior in every sense from a driving perspective.
So really depends what you want. The Z4 3.0si is a rare and good looking car but has a few downsides like the electronic steering and unfortunately the Z4M has all the nice bits that would make a 3.0Si feel more purposeful like the quad exhaust etc but it’s a fabulous car for the money abs without doing too much you can make them really great cars. They are also super reliable with very little issues and service and parts are friendly also tax and insurance are pretty favourable in comparison.
The 987s have the kudos and are really purposeful from a handling and responsive nature, the gearbox is like a bolt action rifle hugely better than in the Z4 and they are fast just don’t really feel that quick which is a sign it’s a great car. Worth testing both and seeing what you think but really if it’s a Cayman S the Z4M coupe is a better comparison and IMO the Z4M would nick it slightly at this level. I would take a 981 over both and a 997 Carrera S over a 981
Hope this helps although a bit rambly, all are great cars really and you can't go wrong as with any used car purchase buying the best your budget allows will reduce money needed to spend and going in eyes open and get the PPI and worce case walk away.
Couple of pics
996 and 991
Porsche 911's, Yorkshire Porsche Festival, Lotherton Hall, Leeds by
Tom Scott, on Flickr
Porsche 911's, Yorkshire Porsche Festival, Lotherton Hall, Leeds by
Tom Scott, on Flickr
Porsche 991, 996 Carrera 4S, Yorkshire Porsche Festival, Lotherton Hall, Leeds by
Tom Scott, on Flickr
991 and the Z4MR
Z&P Eurotrip UK to Monaco 2017 by
Tom Scott, on Flickr
Z&P Eurotrip UK to Monaco 2017 by
Tom Scott, on Flickr
BMW Z4M Roadster, Tatton Park by
Tom Scott, on Flickr
Old Z4M and 997
Porsche 911 Carrera S, Malcesine, Lake Garda, Italy by
Tom Scott, on Flickr
Porsche 911, Sustens Pass, Switzerland by
Tom Scott, on Flickr
IMG_0600 by
Tom Scott, on Flickr
Porsche 911 Carrera S & BMW Z4M Coupe by
Tom Scott, on Flickr
IMG_0109 by
Tom Scott, on Flickr
BMW Z4M Coupe, Silver Grey, CSL wheels by
Tom Scott, on Flickr
the Cayman has the edge in terms of kudos , handling etc but Porsche ownership is a different prospect , ive been there 3 times ( 964 , 996 , 997 ) absolute delight to own + drive but no matter how confident i was in the cars Porsche paranoia is hard to ignore & you always wonder how far away you are from a unexpected bill 
tried to find it but it seems it has fallen off the face of the earth probably been written off 
