lines = open('file2.txt').readlines()
for s in open('file1.txt'):
    s = s.strip()
    print s
    print '\n'.join([l for l in lines if l.find(s) != -1])
    print ''

>>> lines = open('file2.txt').readlines()
>>> lines
['python\n', 'php\n', 'ruby\n', 'cron\n', 'delay\n', 'some other non-interesting string\n', 'ada\n', 'daemon\n', 'decomposition\n']
>>> for s in open('file1.txt'):
...     s = s.strip()
...     print s
...     print ''.join([l for l in lines if l.find(s) != -1])
... 
a
delay
ada
daemon

b
ruby

c
cron
decomposition

import sys
sys.stdout = open('file3.txt', 'w')

import sys

def load_file(file_name):
    lines = list()
    with open(file_name) as fd:
        for line in fd:
            line = line.strip()
            if line:
                lines.append(line)
    return lines

def process_files(key_file, values_file):
    keys = load_file(key_file)
    vals = load_file(values_file)
    data = dict()

    for key in keys:
        for val in vals:
            if key in val:
                data.setdefault(key, list()).append(val)
    return data

def put_results(res, fout=sys.stdout):
    for dkey, dval in res.iteritems():
        fout.write("%s\n"%dkey)
        for ival in dval:
            fout.write("%s\n"%ival)
        fout.write('\n')

processed = process_files('file1', 'file2')

#print results
put_results(processed)

#write to file
my_out = open('file_out', 'w')
put_results(processed, my_out)
my_out.flush()
my_out.close()

>>> ================================ RESTART ================================
>>> 
п»їa

b
ruby

c
cron
decomposition

#print '\n'.join([l for l in lines if l.find(s) != -1])