Tops are graded by appearance. Bear claw used to be considered a defect and thus it resulted in those boards getting a lower grade. The pricier models got the higher grade woods and thus got less bear claw. More recently, people have recognized that bear claw, especially when extensive and symmetrical, is very attractive. Also, Dana Bourgeois, who is something of an expert on top voicing, argues that bear claw tends to occur in trees that yield stiffer wood with a higher sound velocity, which he considers desirable properties for tops (because their stiffness allows them to be shaved thinner and that, coupled with the higher sound velocity, makes them very responsive). So suddenly, bear claw is a good thing.
Run out happens for two reasons: either the wood wasn't perfectly quarter sawn or the grain in the log didn't run parallel to the quarter plane. By all accounts, it has no impact on tone. Some consider it a minor cosmetic imperfection, in the same way that silking is considered a cosmetic enhancement. Silking (evidence of lateral tubules in the wood) indicates wood that has been cut perfectly on the quarter (i.e., perfectly on a plane passing through the center of the log).
Run out occurs when the tubular wood fibers don't terminate at the edge of the board but at the surface. It's as if the tubule has its origin slightly behind the plane of the guitar top at one end of the board and slightly in front of that plane at the other end. The cut didn't run exactly parallel to the axis of the tubules but at a slight angle.
Imagine a great big clump of soda straws, bundled together like a log with the openings at top and bottom and then imagine taking a machete and making an angular, downward slash that enters the "log" of straws at about the middle and exits at the bottom -- kind of like you'd do to make the bottom end wedge-shaped. So the top half is still more or less cylindrical and the bottom half is curved on the back but flat on the front, getting progressively thinner front-to-back as you work your way down. What you'd then have is a clump of straws whose top half revealed the convex, outer surfaces of the straws and whose lower half (below the start of the slash) revealed the concave inner surfaces of straws that had their front portion cut away by the machete slash. If you shone a light from above, it would reflect more off of the upper half than the bottom half, where each concave straw surface would create some shadow.
A board that is bookmatched has been split longitudinally. If the tubules aren't exactly parallel to the split, then they get cut in a manner similar to the straws. When laid open, the two boards have opposite orientations, with the slash closest to the surface of the tubules at the top of one board and at the bottom of the other (because the slash was angular). So, when the light is bouncing off of the bottom of one side (thus looking lighter), it's falling into the nooks and crannies (and looking darker) on the bottom portion of the other side of the guitar top. Change the angle of the light and the light-dark orientation will reverse. This is called a harlequin pattern because often, at the top half of the guitar, the left will be light while the right is dark; and at the bottom half, the pattern will be reversed. this reminded someone of the classic clown Harlequin, who wore an outfit with similar reverse dark-light patterns at the top and bottom halves.
My personal an ever-so-slightly uneven miter joint for the binding in a particularly tricky area, like the headstock of a Guild. It isn't going to affect the tone at all. If it's small, you might not be able to even see it unless you look with a magnifier. It would be better for there not to be any unevenness but if there were, it wouldn't be a big issue. Now consider (hypothetically) an instrument that sounded just as good as your Guild but cost half as much. A binding joint imperfection on such a guitar would be even less of an issue. Even with a significant binding issue, such a guitar would be a spectacular deal, to put it mildly. Now consider an instrument that sounded just like your Guild but cost twice as much. At that price premium, even a teeny imperfection in a binding joint would be very irritating to me.
Run out is kind of the same. At some price point, a higher standard of perfection is a reasonable expectation but at no price point does run out actually change the sound of a guitar. I'd rather not have it (especially as the price of a guitar climbs) but it wouldn't be a deal breaker on a top quality factory-built guitar I otherwise liked. You'll see it frequently on Martins, guilds, Taylors, etc. you probably won't on most Goodalls, Bourgeoises, Froggy Bottoms, etc. But it in no way signifies an inferior instrument.
