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You could define a pretty-printing function:

def print3(n):
    # add commas every third digit from the right
    s = ''
    for k, d in enumerate(str(n)[::-1]):
        if k%3 == 0: s += ','
        s += d
    print s[:0:-1]

and use it to print your numbers:

sage: print3(100)
100
sage: print3(1000)
1,000
sage: print3(10000)
10,000
sage: print3(100000000000)
100,000,000,000