The whole "cheap" Porsche thing doesn't really exist in my experience. Running costs of a 996 can be just as much as a 993 or 997, despite being a fraction of the price. For that reason, I can't really say a 996, 987 or 986 is undervalued. (Written as a 986 Owner who previously thought otherwise. My car has less than 50k miles on it, is in quite great condition and has cost me quite a bit more than I would have expected. If you don't have the equipment or space to do work yourself, I would honestly avoid any Porsche unless you have considerable disposable income)
In my opinion these are the tremendously undervalued (and underappreciated, I might add) cars of today. My rules were: cheap to buy
AND cheap to run.
#1 Nissan 350Z (DE + HR engine types):
-These things are seriously fast, an HR would probably outrun any non-turbo, non GT 996. The DE has a lot of torque on balance. Yeah the ergonomics and 10/10 driving experience isn't great, but they are damn good. They are also incredibly cheap in the US. Cream of the crop Nismo variants can even be had under $20k in good condition.
(The 370z should also be mentioned, but I think the 350z is a more entertaining & accessible car and I think it will also age much, much better).
#2 Mazda RX-8
-Yes, the maintenance on these is a little on the high side. But it can't be more expensive to run than a 15 year old Porsche. But the chassis is sooooo good, and where else can you get a car that handles so well that can fit 4 adults. I've seen RX-8's for as low as $3500 with a clean title. That's nuts.
#3 Scion FR-S.
-Tremendous value even when new, these cars have nosedived in terms of depreciation. I've seen clean relatively low mileage cars for below $13k. How does nobody else see modern day Alfa Giulia GTA or E30 M3? That's basically what the ZN6 twins are. There are few new cars you can go out and buy today that have this much character, in my opinion.
#4 Honda S2000
-I'll admit these aren't quite as good of value as they were 5 years ago, but you're still getting near-Ferrari-levels of manic athleticism and verve from a $10-20k
Honda.
#5 Infiniti G35 Sedan
-You say E36 M3, I say G35 Sedan, first generation. Much nicer interior, more power (in the US). Yeah so it's not as focused as an M3, but all the basic bits are there. Oh and they are stupidly cheap with tons and tons available. Watch out for the salvage titles...
#6 Honda Prelude (last generation)
-I think these are the real sleeper Honda. Nobody has really picked up on them yet, but I think it's coming. They have a really, really great design in my opinion, one of Honda's best and everything that was great about late 90s/early 00s car design -- simple detailing with an apparent lack of mass and athletic overall form. The driving experience is pretty unique too, especially in SH guise, with the front end vectoring you out of tight corners. If the SH had been badged as a Type R, they would already be worth $25k.
#7 300ZX Twin Turbo
-It seems a little crazy that the Supra TT has skyrocketed in value and the very-similar 300ZX has gone almost nowhere. You'd be a fool to spend $45k on a Supra over an equivalent 300ZX for $15k, in my opinion. Looks better too. I realize the Z32 can be difficult to maintain due to the tight engine bay, but the engine itself is robust.
#8 Lexus SC300/SC400
-Considering what you get and how cheap these are, I have to say they are undervalued. The 2JZ or 1UZ engine will run forever and either is perfectly suited to this bargain priced continent crusher. The styling has not yet hit classic status yet, but it's surely almost there. Quality, refinement, comfort, and an airey 90s lack of concern. Take me home Lexus SC300.
(Special mention to the second-gen Lexus GS as well. Such a handsome & stately looking car and much better put together than the Mercedes Benz E class of the time.)
#9 Infiniti M35 (Y34 Model)
-Just a damn-handsome Luxury sedan that we only got for 2 years. A paltry few were sold. Is there a better looking sedan from this time period? I don't think there is...it just looks so...resolved. Haven't checked prices on these in a while, but surely they are cheap.
My list is entirely Japanese, and for good reason. Japanese cars are really, really good and yet somehow they tend to depreciate far more than their European equivalents. Great for me!
