var numeric = [
    ['input1','input2'],
    ['input3','input4']
];
numeric[0][0] == 'input1';
numeric[0][1] == 'input2';
numeric[1][0] == 'input3';
numeric[1][1] == 'input4';

var obj = {
    'row1' : {
        'key1' : 'input1',
        'key2' : 'input2'
    },
    'row2' : {
        'key3' : 'input3',
        'key4' : 'input4'
    }
};
obj.row1.key1 == 'input1';
obj.row1.key2 == 'input2';
obj.row2.key1 == 'input3';
obj.row2.key2 == 'input4';

var mixed = {
    'row1' : ['input1', 'inpu2'],
    'row2' : ['input3', 'input4']
};
mixed.row1[0] == 'input1';
mixed.row1[1] == 'input2';
mixed.row2[0] == 'input3';
mixed.row2[1] == 'input4';

http://jsfiddle.net/z4Un3/

And if you're wanting to store DOM elements:

var inputs = [
    [
        document.createElement('input'),
        document.createElement('input')
    ],
    [
        document.createElement('input'),
        document.createElement('input')
    ]
];
inputs[0][0].id = 'input1';
inputs[0][1].id = 'input2';
inputs[1][0].id = 'input3';
inputs[1][1].id = 'input4';

Not real sure how useful the above is until you attach the elements. The below may be more what you're looking for:

<input text="text" id="input5"/>
<input text="text" id="input6"/>
<input text="text" id="input7"/>
<input text="text" id="input8"/>    
var els = [
    [
        document.getElementById('input5'),
        document.getElementById('input6')
    ],
    [
        document.getElementById('input7'),
        document.getElementById('input8')
    ]
];    
els[0][0].id = 'input5';
els[0][1].id = 'input6';
els[1][0].id = 'input7';
els[1][1].id = 'input8';

http://jsfiddle.net/z4Un3/3/

Or, maybe this:

<input text="text" value="4" id="input5"/>
<input text="text" value="4" id="input6"/>
<br/>
<input text="text" value="2" id="input7"/>
<input text="text" value="4" id="input8"/>

var els = [
    [
        document.getElementById('input5'),
        document.getElementById('input6')
    ],
    [
        document.getElementById('input7'),
        document.getElementById('input8')
    ]
];

var result = [];

for (var i = 0; i < els.length; i++) {
    result[result.length] = els[0][i].value - els[1][i].value;
}

Which gives:

[2, 0]

In the console. If you want to output that to text, you can result.join(' ');, which would give you 2 0.

http://jsfiddle.net/z4Un3/6/

EDIT

And a working demonstration:

<input text="text" value="4" id="input5"/>
<input text="text" value="4" id="input6"/>
<br/>
<input text="text" value="2" id="input7"/>
<input text="text" value="4" id="input8"/>
<br/>
<input type="button" value="Add" onclick="add()"/>

// This would just go in a script block in the head
function add() {
    var els = [
        [
            document.getElementById('input5'),
            document.getElementById('input6')
        ],
        [
            document.getElementById('input7'),
            document.getElementById('input8')
        ]
    ];

    var result = [];

    for (var i = 0; i < els.length; i++) {
        result[result.length] = parseInt(els[0][i].value) - parseInt(els[1][i].value);
    }

    alert(result.join(' '));
}

http://jsfiddle.net/z4Un3/8/

var multiArray = [ ['element 0, 0', 'element 0, 1', 'element 0, 2'], ['element 1, 0', 'element 1, 1']];

and so on...

EDIT every single notation in [] is an array, so you just have to combine them into an another array

Practically? Yes. You can create an array of arrays which functions as an 2D array as every item is an array itself:

let items = [
  [1, 2],
  [3, 4],
  [5, 6]
];
console.log(items[0][0]); // 1
console.log(items[0][1]); // 2
console.log(items[1][0]); // 3
console.log(items[1][1]); // 4
console.log(items);

But technically this is just an array of arrays and not a “true” 2D array, as I. J. Kennedy pointed out.

It should be noted that you could keep nesting arrays into one another and so create “multidimensional” arrays.