I have both: 2013 E92 M3 coupe and 2010 E89 Z4 w/ M Sport.
Couple of thoughts:
1. If I was forced to pick one, I would pick the Z4 hands down if (1) I was not a track rat and (2) I had another car that could carry passengers/cargo.
2. The Z4 is, by some margin, a better DD than the M3, due in large part to its fuel economy, size, and low-end torque.
3. The Z4 is the better looking car. My Z4 gets far more attention than my M3 whenever I take it to car events, the dealer, etc. The E89 Z4 is far more rare than an E92 M3 and a lot of people don't even know what they are.
4. The Z4 is much, much cheaper to mod for big power. $3,000 gets you crazy power on the Z4 with downpipes, a tune, an intercooler, and a filter or intake.
In my humble opinion, a Boxster is not special enough of a Porsche to justify the premium over an E89 Z4. If it were a 911 Turbo or a Carrera GTS, sure, but not a Boxster. This is especially true when you consider the virtues of a hardtop in the Z4.
If it were me, I would buy a CPO, low-mileage Z4 35is, then mod the car with the following:
- FMIC
- Downpipes
- Cobb or JB4
- Filter
- KW v3 coilovers
- H&R sway bars
- WaveTrac limited-slip differential
- A set of lightweight, ideally 18" wheels (HRE R40s or Volk TE-37s would be awesome, but Apex would work, too)
- Michelin Pilot Super Sport tires in 235 and 275
You'll still have cash in the bank over the Boxster and you'll have a car that looks better, is faster, and handles as well as a Boxster.