Create an Array with Data from TD Tags

Issue 1: Work on your formatting. It's a lot easier to debug your own code when you indent correctly, use new lines effectively, and use descriptive variable names.

Issue 2: Uncaught TypeError: Cannot set property '0' of undefined on line 19. You're trying to set array1[0][0] when array1[0] isn't an array. You need to make array[0] an array before you try to use it as one, like this:

if(!array1[i]){
    array1[i] = [];
}

This checks if your array exists. If it doesn't, then it is set to an empty array.

Issue 3: Uncaught TypeError: Cannot read property 'innerHTML' of undefined on line 24. Your loop runs from 0 to 8 and myNodeList only goes up to 7. Changing for (var i=0;i<=NumTD;i++) to for (var i=0;i<NumTD;i++) solves this issue by restricting the bounds of the loop.

Issue 4: Messing around with 3 indices (r, c, and i) is unnecessary and doesn't make things any easier. For one, c and i are always equal, so we can run the loop from c = 0 to c < numTD.

Issue 5: Checking if c + 1 is equal to the number of columns is clumsy. Instead, your second dimension should be c % numCol, which is just the remainder of c divided by numCol. It works perfectly here. We can also increment r when c % numCol is 0.

var myNodelist  =   document.getElementsByTagName("td");
var numTD       =   myNodelist.length;
var numTR       =   document.getElementsByTagName("tr").length;

var numCol  =   numTD/numTR;
var array1  =   [];

var r       =   0;

for(var c = 0; c < numTD; c++){
    array1[r]   =   array1[r] || [];

    array1[r][c % numCol]   =   myNodelist[c].innerHTML;

    if(c % numCol){
        r++;
    }
}

Working example

Issue 6: This approach is generally a clumsy way to accomplish the task. It'd be a lot cleaner to grab each row, iterate through them, and grab the individual cells then. Edit: Got this is right before I saw @dc5's edit. His works just as well.

var rows        =   document.getElementsByTagName("tr");
var results     =   [];

for(var i = 0; i < rows.length; i++){
    var cells   =   rows[i].getElementsByTagName("td");

    results[i]  =   [];

    for(var j = 0; j < cells.length; j++){
        results[i][j]   =   cells[j].innerHTML;
    }
}

Working example

With your current logic, you have a couple of problems:

1. array1 is initialized as [[]]
2. r (the row counter) is never incremented
3. Your for loop: for (var i=0;i<=NumTD;i++) should be for (var i=0;i<NumTD;i++)

The values read from the table are always updating the value at array1[0,0] and array1[0,1]

The fix - for the current logic, is to increment r when ever the column counter is reset to zero and to insert a new empty array at the new row if it doesn't already exist.

Code:

var myNodelist = document.getElementsByTagName("td");
var NumTD = (document.getElementsByTagName("td").length);
var NumTR = (document.getElementsByTagName("tr").length);

var NumCol = NumTD / NumTR;
var array1 = []; // <== initialize as empty array
var c = 0;
var r = 0;

for (var i = 0; i < NumTD; i++) {
    array1[r] = array1[r] || [];  // <== If array at row doesn't exist, 
                                  //     initialize it to a new array

    array1[r][c] = myNodelist[i].innerHTML;

    if ((c + 1) == NumCol) {
        c = 0;
        r++; // <== increment the row
    } else {
        c++;
    }
}

jsFiddle demo

The above code could be simplified a bit by querying the table rows first, then iterating the rows, querying the child td's for each found row.

For example:

var rows =  document.getElementsByTagName("tr");
var rowCount = rows.length;
var r, c, cols, colCount;

var array1 = [];

for (r = 0; r < rowCount; ++r) {
    array1[r] = [];

    cols = rows[r].getElementsByTagName("td");
    colCount = cols.length;
    for(c = 0; c < colCount; ++c) {
        array1[r][c] = cols[c].innerHTML;
    }
}

jsFiddle demo