If you're looking for a more general method which ditches biological systems and uses Von Neumann machines, see gethubphagocyte's (now known as trichoplax) excellent answer.
First of all, we've got to establish that mass is not created nor destroyed (unless your werewolf is partially antimatter and your untransformed human has a way of handling astronomically amounts of energy) to work within physics. Additionally, I assume you wouldn't want a general change in density, since a gigantic monster that used to be a little kid wouldn't be very effective if it just started to float into the stratosphere.
No density change:
This means we're not actually gaining/losing
weight (let's call it mass; since that's what I assume you really want to know), we're just getting or dropping more mass. The generally established way to do that is through the digestive system, so that's what I'd suspect is the best way to start.
Werewolves already are known to have the ability to heal upon transformation (I think, I'm not very familiar with them), which hints at a temporarily supercharged metabolism and actually gives some amount of consistency to this theory. What if upon shapeshifting, they begin to eat ferociously as the creature's body kicks into overdrive, rapidly growing/expanding new parts while absorbing others (a mechanism which is already seen in [special tragic circumstances][s]). This would also explain the way that a shapeshifter could reduce their mass, through abortion and eventually excretion, however, it would take a measure of time greater than the few minutes/second associated with shapeshifting.
You could say again, that the body starts to act very rapidly, and absorbs/sheds the unneeded parts quickly, a process which I suspect would be rather painful as well as leaving telltale refuse where it occurs.
Now, if you didn't mind a change in density, different body parts could be destroyed and recreated in lighter forms, such as muscle turning into fat, bones hollowing, large airsacs filling space, etc. It'd lead to some interesting anatomies, and depending on the intelligence of the shapeshifter, could be deliberately used to exploit odd effects (floating/sinking, whatever). Still, there'd be limits on the range of forms which could be assumed by the shifter, since you can only distribute so much mass in so many ways while keeping a functional body.
Additionally, you'd have to worry about some minerals which are used in some structures but not others. Calcium comes to mind, as while you could turn muscle into bone and vice versa, the fiberous muscle bits wouldn't be used, and the bones would be brittle and generally useless. The shifter could have a unique body arrangement which would keep superfluous minerals and elements stored for use later, or it would have to seek out particular foods during the transformation - quite an interesting plot device.
As for the process itself, the creature could turn into an amorphous blob of undifferentiated body tissue with maybe only a brain floating in the center to direct it all. It could form a crystallizes-type structure to protect itself while transforming - getting lots of nasty microbes strewn throughout your future body is probably going to kill you before the monster hunters do, especially if your immune system doesn't expand to fit your new body.
My personal favorite is a rapid growth that leaves the shifter wracked while parts of their body start to degenerate and clot while others start to enlarge or grow, some falling off or just drying up while excess blood and fluids gush out, possibly layers of skin and body tissue falling off while the new body grows inside. Eww.
As pointed out in the comments, the brain would have to be resized/reformed as well, which would make it so that it's quite possible different forms would have different personalities and memory bases. As well, it's also probable that some memories would be lost during each transformation, so that when the shifter changes and changes back, they'd have partial permanent amnesia, made worse with each transformation. There's a high chance that between that, an insatiable drive to start eating before blacking out, and waking up in a pile of raw body parts (also monster hunters in pursuit!), quite a bit of crazy would happen.