This paper is great: http://cbboff.org/UCBoulderCourse/documents/LunarCyclerPaper.pdf
My favorite sentence is this one:
"The trajectories were propagated using Cowell's method and a 7th-Order, 10-cycle Runga-Kutta integration scheme although for some of the near-collision transfers, a variation of parameters method was selected, with mean anomaly as the fast variable, for use during lunar encounter."
Runge-Kutta is as you have found, a method of numerically solving differential equations, or in other words throwing brute force computing power at a problem that is too hard or impossible to solve in closed form using algebra and calculus.
Cowell's method is the direct approach to the orbit numerical integration problem, where you integrate the equations of motion of all the objects directly. In other words you use Newton's law of gravitation to calculate the acceleration of all the objects, then integrate the acceleration to velocity and velocity to position. This commonly not even called Cowell's method, as it has been reinvented probably thousands of times by thousands of different people, including myself.
To do this numerical integration, you can use Euler's method, another straightforward simple algorithm reinvented thousands of times. Say you know the vector position and velocity of an object, and can use universal gravity and perhaps other effects to find the acceleration. We proceed with time steps - one second is a pretty typical size for Earth-orbit problems. Having figured the acceleration, you multiply it by the size of the time step to get the change in velocity, and add it to the velocity vector. Then you multiply the velocity by the time step and add it to the position vector. Repeat thousands of times, and you have integrated the equations of motion.
You can use Runge-Kutta to perform the integrations required. This is just a refinement on the Euler method above, which can dramatically increase accuracy of one step, which you can then use to either get a more accurate answer or take larger steps.
This is contrasted with Encke's method, which integrates the difference between the actual trajectory of a body in a n-body problem with its reference two-body orbit. Cowell is simpler, but Encke may take less computing power to get the same accuracy when the orbit of the body you are interested in (say a spacecraft) is in deep space far from any planet. You use Kepler's equations to propagate the main two-body motion and just integrate the difference from that reference trajectory. Since the perturbations are smaller, you can take larger time steps and still maintain accuracy. The equations of motion themselves are interesting. You still basically have Newton's laws, but instead of gravity from each object attracting your spacecraft to itself, you effectively have the spacecraft being repelled from the reference trajectory, where the force grows stronger, not weaker, as the distance from the reference grows.
A third method, mentioned in the quote above, is variation of parameters (VOP). In this case, the orbital elements themselves are treated as a body. In a perfect two-body system, the orbit elements are constant. When we talk about perturbing an orbit, VOP takes this literally. Its equations of motion describe how things like the periapse distance and inclination change in the presence of a perturbation. The equations of motion are vastly complicated and not related to Newton's laws at all. Derived from, yes. But the periapse has no inertia as we think of it for a physical body. The advantage of this is that in certain cases, the integration
can be done with algebra and calculus. For instance, the "main problem" in low-Earth orbital mechanics, which just considers the Earth as a spheroid and considers the point-mass and J2 effects on an orbit. We use this to design things like sun-synchronous orbits.
The other thing is that when the external effects are small and predictable, you can dramatically reduce the computation requirements. For instance, consider the problem of determining how long it will take a low-Earth orbit to decay. In this case you have to take into account the gravity of the sun, moon, perhaps other planets, solar radiation pressure, and atmospheric drag. This makes the equations of motion quite complicated, requiring Runge-Kutta or some other integrator to handle. It takes 1000 time steps per orbit to maintain good accuracy with Cowell's method, perhaps somewhat less perhaps with Encke, but VOP can take one time step every 10 orbits!
So to summarize, I have discussed three kinds of equations of motion:
*Cowell's (the direct, obvious approach using Newton's laws of motion)
*Encke's (Integrate the differences only between a reference and actual trajectory)
*Variation of Parameters (Equations of motion of the orbit elements themselves)
and three kinds of integrators
*Closed form integration - Completely accurate when possible, but almost never possible and very difficult when it is - requires lots of pencil and paper
*Euler's method - the obvious numerical integration method
*Runge-Kutta - a more complicated but more accurate numerical integration method.
In theory you can mix and match any equation of motion with any integrator.