Simply put multidimensional arrays are similar to a table in DBMS.
Array of Array (jagged array) lets you have each element hold another array of the same type of variable length.

So, if you are sure that the structure of data looks like a table (fixed rows/columns), you can use a multi-dimensional array. Jagged array are fixed elements & each element can hold an array of variable length

e.g. Psuedocode:

int[,] data = new int[1,1];
data[0,0] = 1;
data[0,1] = 2;
data[1,0] = 3;
data[1,1] = 4;

Think of the above as a table:

1 | 2
3 | 4

int[][] jagged = new int[2][];
jagged[0] = new int[4] {  1,  2,  3,  4 };
jagged[1] = new int[2] { 11, 12 };
jagged[2] = new int[3] { 21, 22, 23 };

Think of the above as each row having variable number of columns:

 1 |  2 |  3 | 4
11 | 12
21 | 22 | 23

A multidimensional array is forms a nice linear layout while a jagged array implies a several extra levels of indirection.

Looking up the value jagged[3][6] in a jagged array var jagged = new int[10][5] works like this: Look up the element at index 3 (which is an array) and look up the element at index 6 in that array (which is a value). For each dimension in this case, there's an additional look up (this is an expensive memory access pattern).

A multidimensional array is laid out linearly in memory, the actual value is found by multiplying together the indexes. However, given the array var mult = new int[10,30] the Length property of that multidimensional array returns the total number of elements i.e. 10 * 30 = 300.

The Rank property of a jagged array is always 1, but a multidimensional array can have any rank. The GetLength method of any array can be used to get the length of each dimension. For the multidimensional array in this example mult.GetLength(1) returns 30.

Indexing the multidimensional array is faster e.g. given the multidimensional array in this example mult[1,7] = 30 * 1 + 7 = 37, get the element at that index 37. This is a better memory access pattern because only one memory location is involved, which is the base address of the array.

A multidimensional array therefore allocates a continuous memory block, while a jagged array does not have to be square like. e.g. jagged[1].Length does not have to equal jagged[2].Length which would be true for any multidimensional array.

Preformance

Performance wise, multidimensional arrays should be faster. A lot faster, but due to a really bad CLR implementation they are not.

 23.084  16.634  15.215  15.489  14.407  13.691  14.695  14.398  14.551  14.252 
 25.782  27.484  25.711  20.844  19.607  20.349  25.861  26.214  19.677  20.171 
  5.050   5.085   6.412   5.225   5.100   5.751   6.650   5.222   6.770   5.305

The first row are timings of jagged arrays, the second shows multidimensional arrays and the third, well that's how it should be. The program is shown below, FYI this was tested running mono. (The windows timings are vastly different, mostly due to the CLR implementation variations).

On windows, the timings of the jagged arrays are greatly superior, about the same as my own interpretation of what multidimensional array look up should be like, see 'Single()'. Sadly the windows JIT-compiler is really stupid, and this unfortunately makes these performance discussions difficult, there are too many inconsistencies.

These are the timings I got on windows, same deal here, the first row are jagged arrays, second multidimensional and third my own implementation of multidimensional, note how much slower this is on windows compared to mono.

  8.438   2.004   8.439   4.362   4.936   4.533   4.751   4.776   4.635   5.864
  7.414  13.196  11.940  11.832  11.675  11.811  11.812  12.964  11.885  11.751
 11.355  10.788  10.527  10.541  10.745  10.723  10.651  10.930  10.639  10.595

Source code:

using System;
using System.Diagnostics;
static class ArrayPref
{
const string Format = "{0,7:0.000} ";
static void Main()
{
    Jagged();
    Multi();
    Single();
}
static void Jagged()
{
const int dim = 100;
for(var passes = 0; passes < 10; passes++)
{
var timer = new Stopwatch();
timer.Start();
var jagged = new int[dim][][];
for(var i = 0; i < dim; i++)
{
    jagged[i] = new int[dim][];
    for(var j = 0; j < dim; j++)
    {
        jagged[i][j] = new int[dim];
        for(var k = 0; k < dim; k++)
        {
            jagged[i][j][k] = i * j * k;
        }
    }
}
timer.Stop();
Console.Write(Format,
    (double)timer.ElapsedTicks/TimeSpan.TicksPerMillisecond);
}
Console.WriteLine();
}
static void Multi()
{
const int dim = 100;
for(var passes = 0; passes < 10; passes++)
{
var timer = new Stopwatch();
timer.Start();
var multi = new int[dim,dim,dim];
for(var i = 0; i < dim; i++)
{
    for(var j = 0; j < dim; j++)
    {
        for(var k = 0; k < dim; k++)
        {
            multi[i,j,k] = i * j * k;
        }
    }
}
timer.Stop();
Console.Write(Format,
    (double)timer.ElapsedTicks/TimeSpan.TicksPerMillisecond);
}
Console.WriteLine();
}
static void Single()
{
const int dim = 100;
for(var passes = 0; passes < 10; passes++)
{
var timer = new Stopwatch();
timer.Start();
var single = new int[dim*dim*dim];
for(var i = 0; i < dim; i++)
{
    for(var j = 0; j < dim; j++)
    {
        for(var k = 0; k < dim; k++)
        {
            single[i*dim*dim+j*dim+k] = i * j * k;
        }
    }
}
timer.Stop();
Console.Write(Format,
    (double)timer.ElapsedTicks/TimeSpan.TicksPerMillisecond);
}
Console.WriteLine();
}
}

Multi-dimension arrays are (n-1)-dimension matrices.

So int[,] square = new int[2,2] is square matrix 2x2, int[,,] cube = new int [3,3,3] is a cube - square matrix 3x3. Proportionality is not required.

Jagged arrays are just array of arrays - an array where each cell contains an array.

So MDA are proportional, JD may be not! Each cell can contains an array of arbitrary length!