Binary clock version two, reimplemented to be shorter

binaryClock2.js

function pad(str,num) { return str.length < num ?  pad(0 + str,num) : str; }

function binaryClock(d) {
	var bin = (pad('' + d.getHours(),2)
		+ pad('' + d.getMinutes(),2) 
		+ pad('' + d.getSeconds(),2) ).split('') //string of time digits to array
		.map(function (n) { return pad((+n).toString(2),4) }), //conv to binary and pad
	i,j,str=''; 
	for (i = 0; i<4; i++) {
		for (j = 0; j<bin.length; j++) {
			str += bin[j][i];
		} str += '\n'; }

	return str
}
console.log(binaryClock(new Date()));

• The recursive padding is clever, since you're expecting little padding.
• Line 8 looks like the beginning of a statement. It isn't, but to notice that you have to distinguish between , and ; at the end of line 7 before the comment. You could just use a second var, or you could indent line 8 more. I think I'd use a second var statement and put a blank line before it, so the function has two parts (calculating, then reorienting).
• The function that converts a single digit to BCD looks squeezed in. I'm not sure it's quite simple enough to be inline (though maybe it's just the punctuation in (+n) that bothers me) — plus, if you pulled it out and gave it a name, the code would be more self-documenting.
• There are two places the number 4 comes up (for the bit-length of a BCD digit) that look like magic.
• The formatting of line 12 looks odd. And line 14 is wanting a semicolon.