When I see knot tables, I have two feeling: ah, it's beautiful, and… painful.
I don't see how knots are ordered in the knot table, the way to go from one knot of a certain crossing number to another seems to be completely random. But I would guess there are some order? For example, why are the Perko pair put next to each other even before people knew they are the same?
In short, if the word "periodic table" seems confusing, my real question is, how are the knots in knot table ordered?
Best Answer
Just for kicks, here's a partial list of various ways some people like to occasionally think of as ways of sorting knots.
Knot energies. For example, the electrostatic potential on knots in $S^3$ is a real-valued function on the space of knots in $S^3$ such that there's only finitely-many knot types below any given energy level. See papers of Freedman, He and Wang, like Möbius invariance of knot energy, also Jun O'Hara. But there are many other knot energies out there in the literature.
Crossing number + ??. The traditional knot table. Closely related are things like bridge numbers. Minimal number of tetrahedra in a triangulation of the complement. Stick number. Degree of a polynomial or trig function that it takes to represent the knot, and so on.
Geometrization (as I mentioned in my comments above). See also Daniel's comment.
Geometrization + the geometrization of the 2-sheeted cyclic branched cover of $(S^3,K)$. This is related to "arborescent knots". Similarly, this leads to all kinds of variant ideas. See the big paper of Bonahon and Siebenmann. This is also related to rational tangle decompositions of knots.
Braid index + a canonical form for conjugacy classes in the braid group.
Plat closures + canonical representatives of double-cosets of the Hilden / wicket subgroup. This would be a refinement of the bridge number description.
You could sort knots based on various knot invariants. Alexander polynomials and Jones polynomials being fairly popular ones.
edit: Ken Perko wrote to me to object to my first comment (top of the page, before my answer). His comment deserves a post of his own but until that happens, I'll quote him here: