I wrote a Python script for this purpose that utilizes difflib.SequenceMatcher:
#!/usr/bin/python3
from difflib import SequenceMatcher
from itertools import tee
from sys import stdin
def pairwise(iterable):
    """s -> (s0,s1), (s1,s2), (s2, s3), ...
    https://docs.python.org/3/library/itertools.html#itertools-recipes
    """
    a, b = tee(iterable)
    next(b, None)
    return zip(a, b)
def color(c, s):
  """Wrap string s in color c.
  Based on http://stackoverflow.com/a/287944/1916449
  """
  try:
    lookup = {'r':'\033[91m', 'g':'\033[92m', 'b':'\033[1m'}
    return lookup[c] + str(s) + '\033[0m'
  except KeyError:
    return s
def diff(a, b):
  """Returns a list of paired and colored differences between a and b."""
  for tag, i, j, k, l in SequenceMatcher(None, a, b).get_opcodes():
    if tag == 'equal': yield 2 * [color('w', a[i:j])]
    if tag in ('delete', 'replace'): yield color('r', a[i:j]), ''
    if tag in ('insert', 'replace'): yield '', color('g', b[k:l])
if __name__ == '__main__':
  for a, b in pairwise(stdin):
    print(*map(''.join, zip(*diff(a, b))), sep='')
Example input.txt:
108  finished   /tmp/ts-out.5KS8bq   0       435.63/429.00/6.29 ./eval.exe -z 30
107  finished   /tmp/ts-out.z0tKmX   0       456.10/448.36/7.26 ./eval.exe -z 30
110  finished   /tmp/ts-out.wrYCrk   0       0.00/0.00/0.00 tail -n 1
111  finished   /tmp/ts-out.HALY18   0       460.65/456.02/4.47 ./eval.exe -z 30
112  finished   /tmp/ts-out.6hdkH5   0       292.26/272.98/19.12 ./eval.exe -z 1000
113  finished   /tmp/ts-out.eFBgoG   0       837.49/825.82/11.34 ./eval.exe -z 10
Output of cat input.txt | ./linediff.py:
