Sampling words from randomly chosen text files
Since your code performs multiple things at once, you should split it into functions for readability. A first naive rewrite can yield:

from collections import Counter
import random


def filter_text(text):
    return (text
            .replace('\n', ' ')
            .replace('\xa0', '')
            .replace('  ', '')
            #Removing these automated notifications
            .replace('Wichtiger Hinweis:Diese Website wird in älteren Versionen von Netscape ohne graphische Elemente dargestellt. Die Funktionalität der Website ist aber trotzdem gewährleistet. Wenn Sie diese Website regelmässig benutzen, empfehlen wir Ihnen, auf Ihrem Computer einen aktuellen Browser zu installieren.Zurück zur Einstiegsseite Drucken Grössere Schrift', '')
            .replace('Vorwärts ähnliche Leitentscheide suchenähnliche Urteile ab 2000 suchen Drucken nach oben', '')
            .replace('Bundesgericht Tribunal fédéral Tribunale federale Tribunal federal', '')
            .replace('Navigation Neue Suche Zurück zum Suchresultat Rang: Zurück 180', '')
            .replace('Navigation Neue Suche Zurück zum Suchresultat Rang:1 ähnliche Leitentscheide suchenähnliche Urteile ab 2000 suchen Drucken nach oben', '')
            .replace('  ', ' '))


def create_string_from_files(files, root='txt_sr_de/txt_sr_de', sample=50):
    #creating random list
    random_list = []
    for item in range(sample):
       list_item = random.choice(files)
       random_list.append(list_item)

    #creating long string
    long_str = ''
    for de in random_list:

        input_file = open(os.path.join(root, de), 'r')
        text = input_file.read()

        long_str = long_str + filter_text(text)
    return long_str


def extract_most_common_sequence(text, minimum_occurences=3, times=3):
    for n in range(1,int(len(text)/times+1)):
        substrings=[text[i:i+n] for i in range(len(text)-n+1)]
        freqs=Counter(substrings)
        if freqs.most_common(1)[0][1] &lt; minimum_occurences:
            n-=1
            return seq
        else:
            seq=freqs.most_common(1)[0][0]


def main(files, repeat=100):
    str_seq_list = []

    for str_seq in range(repeat):  
        long_str = create_string_from_files(files)
        str_seq_list.append(extract_most_common_sequence(long_str))

    return str_seq_list


if __name__ == '__main__':
    import pickle
    de_list_soz = pickle.load(open('de_list_soz.p', 'rb'))
    str_seq_list = main(de_list_soz)
    pickle.dump(str_seq_list, open('SOZIALRECHT_DE.p', 'wb'))


Now we can start cleaning things up.

In create_string_from_files, you are basically reinventing random.sample:

&gt;&gt;&gt; import random
&gt;&gt;&gt; random.sample('abcdefghi', 4)
['h', 'e', 'c', 'f']


You also happen to open files but never close them: use the with statement to automatically handle that.

Lastly, concatenating long sentences manually is not memory efficient. Let's ask str.join to do it for us for now. But in order to do it nicely, we need to split the function further:

def read_and_filter_file(filename):
    with open(filename) as input_file:
        text = input_file.read()
    return filter_text(text)


def create_string_from_files(files, root='txt_sr_de/txt_sr_de', samples=50):
    return ''.join(
        read_and_filter_file(os.path.join(root, de))
        for de in random.sample(files, samples)
    )


The same kind of improvements can be made to the main function by replacing the "create empty list + for loop + append" template by a more efficient list-comprehension:

def main(files, repeat=100):
    return [
        extract_most_common_sequence(create_string_from_files(files))
        for _ in range(repeat)
    ]


The extract_most_common_sequence function can also be optimized by using some itertool recipe. I’m thinking about a variation of the pairwise recipe since your list-comprehension, with n being 2 is pretty much it. i.e. using:

&gt;&gt;&gt; long_str = 'This is a test'
&gt;&gt;&gt; n = 2
&gt;&gt;&gt; [long_str[i:i+n] for i in range(len(long_str)-n+1)]
['Th', 'hi', 'is', 's ', ' i', 'is', 's ', ' a', 'a ', ' t', 'te', 'es', 'st']
&gt;&gt;&gt; n = 4
&gt;&gt;&gt; [long_str[i:i+n] for i in range(len(long_str)-n+1)]
['This', 'his ', 'is i', 's is', ' is ', 'is a', 's a ', ' a t', 'a te', ' tes', 'test']


So using something like:

def tuplewise(iterable, length):
    tees = itertools.tee(iterable, length)
    for i, t in enumerate(tees):
        for _ in xrange(i):
            next(t, None)
    return itertools.izip(*tees)


For Python 2 or:

def tuplewise(iterable, length):
    tees = itertools.tee(iterable, length)
    for i, t in enumerate(tees):
        for _ in range(i):
            next(t, None)
    return zip(*tees)


for Python 3, you can simplify the writting and save a bit on memory usage like so:

def extract_most_common_sequence(text, minimum_occurences=3, times=3):
    sequence = ''
    for n in range(1, int(len(text)/times+1)):
        freqs = Counter(tuplewise(text, n))
        (most_frequent, higher_frequency), = freqs.most_common(1)
        if higher_frequency &lt; minimum_occurences:
            break
        sequence = ''.join(most_frequent)
    return sequence


Now I defined sequence = '' as a security measure in the unlikely event that the text is quite short an no letter appear more than twice. It's just to make the function return something in each and every cases.



Now that the code is more readable, let's tackle that memory issue of yours.

The thing to note is that aggregating the content of 50 files in one single string in memory is likely to blow things up. So instead, let's use some disk storage. We'll use the tempfile module for that. The idea is to store the filtered bits of text into a single file and read that file (over and over again) to get the desired most common sequence. We thus need to adapt our tuplewise a bit to either read one character at a time and yield words of the requested size or, better as I/O is concerned, repeatedly read a block of data of a fixed size and grab caracters out of it one by one to produce words of the desired size:

import os
import random
import itertools
import tempfile
from collections import Counter


def filter_text(text):
    return (text
            .replace('\n', ' ')
            .replace('\xa0', '')
            .replace('  ', '')
            #Removing these automated notifications
            .replace('Wichtiger Hinweis:Diese Website wird in älteren Versionen von Netscape ohne graphische Elemente dargestellt. Die Funktionalität der Website ist aber trotzdem gewährleistet. Wenn Sie diese Website regelmässig benutzen, empfehlen wir Ihnen, auf Ihrem Computer einen aktuellen Browser zu installieren.Zurück zur Einstiegsseite Drucken Grössere Schrift', '')
            .replace('Vorwärts ähnliche Leitentscheide suchenähnliche Urteile ab 2000 suchen Drucken nach oben', '')
            .replace('Bundesgericht Tribunal fédéral Tribunale federale Tribunal federal', '')
            .replace('Navigation Neue Suche Zurück zum Suchresultat Rang: Zurück 180', '')
            .replace('Navigation Neue Suche Zurück zum Suchresultat Rang:1 ähnliche Leitentscheide suchenähnliche Urteile ab 2000 suchen Drucken nach oben', '')
            .replace('  ', ' '))


def read_and_filter_file(filename):
    with open(filename) as input_file:
        text = input_file.read()
    return filter_text(text)


def create_string_from_files(output, files, root='txt_sr_de/txt_sr_de', samples=50):
    for filename in random.sample(files, samples):
        output.write(read_and_filter_file(os.path.join(root, filename)))


def read_chunks(file_object, chunk_size, block_size=4096):
    word = file_object.read(chunk_size)
    yield word
    while True:
        data = file_object.read(block_size)
        if not data:
            return
        for character in data:
            # Drop first character and append the next one
            word = word[1:] + character
            yield word


def extract_most_common_sequence(input_file, minimum_occurences=3, times=3):
    input_file.seek(0, os.SEEK_END)
    file_size = input_file.tell()
    sequence = ''

    for n in range(1, int(file_size/times+1)):
        input_file.seek(0)  # Be sure to read the whole file each time
        freqs = Counter(read_chunks(input_file, n))
        (most_frequent, higher_frequency), = freqs.most_common(1)
        if higher_frequency &lt; minimum_occurences:
            break
        sequence = most_frequent
    return sequence


def main(files):
    with tempfile.NamedTemporaryFile(mode='w+') as storage:
        create_string_from_files(storage, files)
        return extract_most_common_sequence(storage)


if __name__ == '__main__':
    import pickle
    de_list_soz = pickle.load(open('de_list_soz.p', 'rb'))
    str_seq_list = [main(de_list_soz) for _ in range(100)]
    pickle.dump(str_seq_list, open('SOZIALRECHT_DE.p', 'wb'))


I changed main into returning a single element rather than a whole list as it feels cleaner with this implementation. The whole repetition thing is done in the test code now.