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!

The sub is a Paradigm Servo-15 placed against the center of the 22' front wall, 3' behind the main speakers.
The mains are B&W CDM 9NT crossed over at 80hz @ 60º Phase.

I'm currently using a 35hz crossover @ 30º Phase, and the results are slightly better if I can accept the slight reduction in 20hz extension.
The new phase angle seems to partially mitigate the 50-60hz hump and 80hz null. (the hump begins to reappear if the level is raised much further though)

BTW, if I have one nit to pick with the Servo-15, it's that it's frequency range is too broad. A steeper crossover filter at 35hz would be nice for integrating with large speakers. The bass is extremely clean and effortless at high SPL though.

50z crossover @ 30º:
db - hz - (deviation from 1khz reference; db)
69 - 20 - (-6)
72 - 25 - (-3)
74 - 31 - (-1)
75 - 40 - (0)
74 - 50 - (-1)
74 - 63 - (-1)
71 - 80 - (-4)
76 - 100 - (+1)
67 - 125 - (-8)
72 - 160 - (-3)
73 - 200 - (-2)