Remainders are books which have been discounted by the publisher and marked to differentiate them from regular sales.
Firstly, let’s explore what remainder marks are. They come in different styles and are sometimes located in different places. The most commonly used remainder mark is made with a black magic marker (felt pen) and is a dot or line on the bottom page edge, usually near the spine. Occasionally it can be found on the top page edge and rarer still, the side page edge. Doubleday and some other publishers used to spray the bottom page edges with a red ink that gave a speckled effect. Random House would sometimes use a small ink stamp with their ‘house’ logo. Simon and Schuster would use a similar stamp with their trademark ‘sower’ logo. Putnam used a capital ‘P’ ink stamp. Other publishers have been known to write an ‘R’ on the front paste down, while still others have placed a stamp on the title page. Years ago, if a paperback was remaindered, a punched hole on the front cover or a scalloped-cut off corner would be the method of identification.

Why would someone deliberately deface a book? And who does this defacing? In all cases, it is the publisher or distributor who marks the books. It is the most efficient way for a publisher to differentiate specific copies of books that are sold to new retailers. So why would a publisher need this information? I mean, one copy is the same as any other. The copy may be the same, but what a retailer paid for it may differ and as it turns out, that is the determining factor.
Let’s say a hardcover book will retail for $25 and the initial print run was 10,000 copies. The standard retailer discount is 40%, so they pay the publisher $15 for each copy and when the book sells, the ten bucks is the bookstore’s cut. So now we fast forward about a year, when the paperback of the same title is about to be released and when there are still, let’s say, 1,000 copies left in the warehouse. The remaining copies of the hardcover still in the publisher’s warehouse get sold off to remainder wholesalers, sometimes called ‘jobbers’, at a discounted price.
These remaindered copies are either books which have been shipped to retailers and returned to the publisher or books which were never shipped anywhere and were untouched in the warehouse. All these copies are then marked by the publisher (as noted above), sold and shipped off to the wholesalers. Now they are listed by the wholesalers and eventually will be sold to retailers: individual independent booksellers, multi-outlet independents, national and regional chain bookstores and also non-traditional book outlets (like big box stores). These copies are then marketed at bargain prices, and in many cases, less than the paperback price of the same title. This also explains why some remaindered copies look dead solid perfect (except for the mark) while others show signs of rubbing to the front and rear panels of the dust-jacket and perhaps some shelf wear. These particular copies were sent to stores, handled by potential customers and then returned to the publishers as unsold.
You may even find books that have been signed by the author at an event in a new bookstore on the remainder tables. The author would have signed copies that the store then had in stock but were later returned to the publisher for credit.
Just keep in mind that if you really care if a book has a remainder mark, you should ask the bookseller, if he hasn’t already mentioned it in his description. If a dealer is selling you a collectible book, marks or stamps of any kind should always be mentioned in the description, so that you can make an informed choice.