I owned both concurrently for some time, and it was a very easy decision to sell the WA3. The crack is more detailed, dynamic and punchy - overall more involving to listen to - and, for the record, I was running some super pricey amperex 7308 pq's (among others) and a 5998 in my Woo. Hd650's sounded good with both amps - albeit substantially better with my crack (even in its stock form). Hd800's also sound great with the crack, whereas the Woo OTL's are, IMO, to slow and tubey sounding to show off what hd800's can really do.
As noted repeatedly here and in the crack thread, particularly with the speedball in place, the crack is simply a better, more sophisticated circuit than what is under the hood in both the WA3 and frankly, the doubly expensive WA2. Neither Woo amp loads the tubes with constant current (unless - you do what head-fi member grindingthud did and go to great lengths to diymod the Woo to copy the crack speedball design!). The Woo chassis are also too small to add film output caps which have a clear impact on the sound quality. Jamie has posted some excellent write ups on this subject in the crack and cap threads if you're interested. For further reference, people used to pay out the nose to put blackgate electrolytics in their woos, but frankly, blackgates suck a phatty when you compare their signal dissipation to even cheap film caps.
All in all, the funds bottlehead allocates to quality components and circuity, woo spends on heavy case work and labor to assemble the amps. There's nothing wrong with that, but if you're willing to pick up an iron and follow the step by step directions, crack far outclasses the WA3 sonically.