Like many other companies Spyderco occasionally produces a knife that, while mechanically safe, falls short of their standards for normal production.  And, like other companies, they choose to sell these "blemished" specimens as, you guessed it, "seconds".   These knives, while perfectly safe to use, carry no warranty.  So, in order that both we and they can distinguish them from first quality, warrantied pieces, they mark them by grinding a notch in the blade.   

Although all that I have seen have this notch on the spine, at least on collector states they have seen photographs of one where the notch is on the choil.  All that I have seen are on what I consider to be the right hand side of the blade.  That is to say, the side that is on the right if you hold the opened/unsheathed knife with the spine on top and the tip pointing away from you.   The notches do vary considerably in shape, but all that I have seen were obviously created intentionally and could not be confused with a "ding" incurred during hard use.  

While these knives can be provide excellent value to someone who is looking for an inexpensive hard use knife, the fact that they are less than perfect, and carry no warranty, does impact their worth.  Thus knowledgeable and honorable sellers will always clearly describe them as seconds.  However, the secondary market does tend to attract a disturbingly large percentage of sellers who lack one or both of those traits.  So it does pay to inspect photographs VERY carefully, and ask questions if you even remotely suspect a mark on the spine or choil may be a notch.   

I will just add that I should learn to follow my own advice.  The picture  at the bottom of this page is the auction photo of the notched Kiwi I purchased.  I saw the "speck" on the spine, but passed it off as just another piece of the same debris on the paper towel or napkin used as a background.  Big mistake.   Seller claimed ignorance.       

Below are photos of notches on a variety of knives.   Some were taken by me, others by fellow Spyderco enthusiasts.   The ones not taken by me are identified with the forum ID of the person who took them.   I hope, with the aid of the Spyderco community to eventually have at least one, and preferably a number of photos here showing the notch on every category of Spyderco knife.

I am normally a stickler when it comes to respecting copyright, but I believe that since I purchased the knife in the photograph, and am using the photo merely to illustrate how difficult the "speck" on the blade is to identify as a notch, due in part to the angle, in part to the lighting, and in part to the choice of background, I believe my use of  it falls under the doctrine of "fair use".    

Here's a SpyderFly notched second.  The Photo courtesy of fellow Spyderco Forum forumite SeanH.   Notice that this notch is located on the lower right tang, rather than on the blade's spine.

Latest addtion to this "rogues gallery" of notched seconds, is this Jigged Bone Micro Dyad.  These photos were lifted from an eBay auction of travis... who has earned the nickname "Dr.FrankenSpyder" on the forums for selling Spydercos pieced together from parts of questionable origin.  While used without permission, once again the doctrine of fair use applies here.  The yellow arrows were added by me, the listing conveniently made no mention of the knife being a second.  Note the small black "spot" the arrows point to.  Without them, and with no indication by the seller that the knife is a second, the notch is fairly easy to miss.