Probably your best bet for Vol 1 & 2 of the war within is through ebay. Vol 2 is pretty cheap, however, vol 1 does sometimes come with a high price tag. If your search abilities are good, however, you can often see people selling their ENTIRE Dreamwave comic collection for pretty cheap... including the individual issues for the War Within.
Vol 3 was never put into trade due to several reasons:
1) Dreamwave went bankrupt. Ergo, the story stopped.
2) Many of the people working on the comic were never PAID for their work. So, there would be some hard feelings on reissuing work that wasn't properly paid for.
3) Reissuing an incomplete comic makes very little sense. It just brings up lots of "why can't you finish it?" questions, which brings me to my next point...
4) The story itself is tied up in legal battles as to who owns the rights to the story. Same as with the Dreamwave G1 story. IDW can properly reissue older Dreamwave comics that were put into trades, but not "loose" issues that still have financial legal problems attached to them.
Could IDW end all this problem by spending alot of money to "buy" the rights to it? Yes, but...
5) The cost to recover the rights to reissue a story that is not really set in the IDW universe would not cover the profit that the comic would make.
While I love the War Within, and would love to see this last story finished, I think the money could be better spent on creating NEW old Cybertron stories in the IDW universe, such as they attempted with Stormbringer and Megatron: Origins.