I feel like being a jerk and quoting myself and then quoting you. As I said at the beginning, a concerted effort should be made to put all of this stuff in print with season box sets. The examples I gave that existed included the 'key to time' series, and then you gave me a link to the key to time series. Wonderful!
The truth is that not a single of the classic doctor's output can be found on DVD in completion and that's because they aren't taking a serious approach to their reissue.
All those other box set you list are scrawny compared to other reissue sets. The Amazon exclusive box you list for instance is 1) only six stories and 2) collects other things that are out of print.
So here we are then...too much stuff out of print, and in general way too expensive to make Dr. Who accessible (I'm not paying $20/story.) Its too bad when the new seasons are way over-priced and they are still cheaper than the classic material from the 60's - 80's. Sheesh.
Edit: to take this to an even greater level of stupidity, here's a decent episode guide (though no season 2 or 3 of the new series.) Really gives some perspective of how doing this in some organized manner (instead of as a bunch of '1 dvd = 1 story' installments.):
http://nitro9.earth.uni.edu/doctor/FAQ/Faq_2.txt
If you do a bit of averaging, you find that most seasons were ~ 6 stories at 4 episodes each (IE 24 episodes of the 25 minute variety), meaning about 6 episodes could fit on a DVD, meaning about 4 discs per season (fairly modest). There are clearly exceptions--some seasons would be closer to 6 DVDs (still very doable) and others only 3.)
At 26 'classic' seasons, that's still a lot of boxes, so they might be wise to consolidate where possible, and of course, some episodes have apparently been lost. Nonetheless, THIS is the way to approach business instead of the manner they are doing it now which keeps the full thing from getting out and keeps these episodes essentially unaffordable/inaccessible to most.