My opinion...avoid getting too obsessive about what gets defragmented and what does not. As long as you get most of it (99%?), the 1% that refuses to defrag isn't going to affect your world, at all. A lot of times these are just active cache files the system uses. So even if you did defrag them, they would be refragged the very next moment you did something on your computer, anyway.
Now if you really must have your way, you could always try booting from a 2nd partition or 2nd HD, and then defrag your original HD. That often does the trick for that last stubborn 1%, once the system that would be using those files is not active during the defrag process. Mind you, this will likely just get refragged when you boot-up in normal configuration, but at least you got a complete defrag once, right?
After that, you have to just let it go that the system is going to want it's own way on a few things. It will still run just as well, either way. So just let it have it's way. You can still find gratification in keeping everything else routinely defragged as you like, thereon.
You should also be aware that there is
some consensus (but not overwhelming consensus) that the modern HD is making its own data location optimizations in the physical domain, anyway. This is in contrast to a defragger app performing data location optimizations in the logical domain (which may end up being completely arbitrary in the physical domain). So some say that defragging is indicative of absolutely nothing. Take it for what you will, or not at all. Just don't freak out over the impact of that "last 1%", given that the whole physical vs. logical domain issue likely will be a far more influencing factor, ultimately.
Now here's something that I would be interested to hear some HD experts weigh in- if you have a 3 partition drive (also assuming single platter), with 1 smaller partition on each "end" and the big one in the middle, is it more advantageous (speed and access-wise) to install your OS at the small partition in the beginning or the small partition at the end of the HD? ...or does it matter, at all? ...or maybe the one in the middle ends up better than either end? :O