Subwoofer calibration quandary...

I hope that I understand your question. If so, there will be many opinions out there, but since you asked......
I believe that it is best to scheive the flatest overall response with a minimum of distortion. Different areas of the room will have different peaks and valleys, so you may have to decide to optimize the response for one or two seats. It is worthwhile to try for +/- 5 dB across the spectrum, but it is difficult to acheive, even with equalizers and room treatments. I would not try to push the sub any lower than it can safely go without distortion (-3 dB). A good sound meter can help plot out your room (tedious) or you can pay for the service. Getting a sub to sound right is difficult and maddening. So much trial and error, but hopefully you will know when its right and actually have some fun trying! Good luck!

Thanks for the response. :)
Here's what I have so far according to my RS meter and Test CD.
Listening (measurement) position is at 3/5ths of both room dimensions.
First-order modes are 25 and 33hz.
The sound of the curve shown is basically weightless in the upperbass, while dinosaur foot-stomps dislodge knick-knacks.
Bass instruments have the requisite grunt, but not much personality.
I can iron out most of the upperbass valleys, but the low and mid bass end up at +9db.

db - hz - (deviation from 1khz reference; db)
73 - 20 - (-2)
74 - 25 - (-1)
74 - 31 - (-1)
74 - 40 - (-1)
77 - 50 - (+2)
76 - 63 - (+1)
66 - 80 - (-9)
72 - 100 - (-3)
64 - 125 - (-11)
71 - 160 - (-4)
72 - 200 - (-3)

In my experience, your measurements are typical. Changing one parameter changes all others. Where is your sub placed in the room and in relation to your mains? What is your crossover point? What main speakers do you use? I find that placing a sub in a corner will excite several modes, depending on where you are sitting. I moved my Hsu VTF-3 out from the corner. It has plenty of volume for my room, so i didn't need to place it in a corner. I think my overall response is smoother. I am using floorstanding Dynaudios which are rated down to 34 Hz (-3 dB) anechoic response. I only use the sub below 50 Hz, so it is easier because I have fewer frequencies to worry about. I can't change my mains' position much, but I did move my sub (80 lbs.) around quite a few times!