I own both, and if you're interested in the nitty-gritty, I did a fairly detailed comparison of distinct features in both cars, which I won't repeat:
http://986forum.com/forums/showthread.php?t=4874
Some broader points to consider, from which you can draw your own conclusion:
* I've driven the SLK280, 350, 55...987 and 987S, Cayman..and Z4M, and the SLK55 was the only car of that bunch that
felt decisively faster than the others in a straight line (376 lb-ft of torque @ 4000 rpm is a face-bender).
* If the car is in any way shared, as you imply, or your wife will be spending alot of time in the car as a passenger, you may find that the visceral experience of driving the Box eventually wears out its welcome. Women (most, not all) don't seem to share the joy in having a flat-six pounding behind the head all the time, particularly top up, and on the east-coast you're obviously going top-up alot more than us lefties.
On a pure sound-dampening basis I'd actually say the 987s three-layer top is as good as the SLK hardtop. However, the hardtop with the front engine layout makes the SLK cabin much more sedate top up. The different aerodynamics of the two cars result in the SLK cabin also being more sedate with the top down (and it has a mesh windscreen, that obviously doesn't rattle

). At speed, the Box will definitely give your wife a bad hair-day. The SLK will not.
* I've not driven the manual SLK (hard to find), but the seven speed automatic is quite good and works well, as the power band is in the lower revs. Pairing an automatic with the Boxster engine (or any other engine where the good-stuff is in the upper RPM range) strikes me as disjointed. That being said, many owners on this board enjoy their Tip and Porsche's pseudo-manual mode is considered good. Pseudo-manual in the SLK pretty much blows.
If you get the manual Boxster, make sure you (and your wife) are comfortable operating the "heavy" pedals and shifter which aren't always the easiest to engage smoothly if you're not in good form on a given day.
* Boxster boarders favorite rebuttal to any comparison is "wait till you drive the twisties." However, the steering on the SLK is quite crisp, and the turn-in is excellent. It's only when compared to the one of the best handling cars in the world does it seem lacking, but obviously a front-engined car can't match the Physics of one that's mid-engined. But how-often does one encounter these "twisties" without seeking them out? And does the marginally enhanced performance of the Box in the twisties alone, justify purchasing it over the SLK? In my mind, the answer is no.
* Servicing the two is a wash. Over a given 65K period, you'll be doing the Box 3 times (20K intervals) and the SLK 6 times (1k which is free, then every 13k). However, your running cost will be roughly comparable in that the Box chews PS2s faster than the SLK chews ContiSports. If spending an
average of $1,500+ every 20-25K concerns you in any way, then get neither and head down to the BMW dealership where they're offering 4yrs/50K of free maintenance. I can't stress enough to prospective "luxury/sport" car buyers the importance of factoring in running costs.
* If I was a Crash Test Dummy, I'd want to be driving the Boxster over the SLK. The ability of the Box to avoid accidents and the stupid shenanigans of other drivers is flat-out amazing. It's pretty much the combination of the handling with the phenomenal brakes. The Box also has more airbags in the event you or a loved one do collide with something, and I have more faith in the top-down roll-over protection of the Box than the SLK, although I suspect a top-down roll-over in either would be fatal. Top-up, obviously the SLK would fare better.
* My parents are in the age bracket just above yours (not attempting to stereotype you on your age, just giving you a third party opinion). My dad is a softcore car enthusiast (SC430, 750i), my mom, not so much, but they have driven both cars extensively when they come out to do the Cali thing. There is no discussion any more. Neither have any interest in driving the Box (but then again, the SLK is more similar to the Lexus roadster than to the Porsche).
* Let me conclude on something of a tangent by saying that I view the Boxster and the 911 convertible to be two separate driving experiences, and the statement that the "Boxster is the poor man's 911" to be misinformed rubbish that would only come from someone who hasn't personally experienced both. I would however, say that the SLK is in fact the poor man's SL, in that there is nothing the SLK does that the SL class doesn't do better.