>>> 'абвг'.encode('cp1251').decode('cp866')
'рсту'
>>>

def load_rules(ifname):
    rules_lst = []
    with open(ifname) as f:
        for line in f:
            print line.decode('cp866')
            continue
            lst = line.strip().split(';')
            name = lst[1].lower()
            expr_from = lst[0].strip('()')
            sublst_to = lst[2].strip('()').split('|')
            rules_lst.append([name, expr_from, sublst_to])
    return rules_lst

# -*- coding: utf-8 -*-

import re

textfile = 'file.txt'
rulesfile = 'rules.txt'
outfile = 'output.txt'

def load_rules(ifname):
    rules_lst = []
    with open(ifname) as f:
        for line in f:
            print line.decode('utf-8')
            continue
            lst = line.strip().split(';')
            name = lst[1].lower()
            expr_from = lst[0].strip('()')
            sublst_to = lst[2].strip('()').split('|')
            rules_lst.append([name, expr_from, sublst_to])
    return rules_lst

#for r in load_rules(rulesfile):
#    print r

def load_text(ifname):
    with open(ifname) as f:
        return next(f).strip()

#print load_text(textfile)

def repl_group(text, rule):
    lst = []
    expr, to_lst = rule[1:]
    for tw in to_lst:
        repl = re.sub(expr, tw, text)
        lst.append(repl)
    return lst

#print repl_group('abcd', [None, 'a|c', ['1', '2', '3']])

rules_lst = load_rules(rulesfile)
text = load_text(textfile)

out_lst = repl_group(text, rules_lst[0])
for t in (i for i in repl_group(text, rules_lst[2]) if i not in out_lst):
    out_lst.extend(repl_group(t, rules_lst[0]))

out_lst = [i.decode('utf-8') for i in out_lst]

print u'; '.join(out_lst)

out_lst = [i.decode('utf-8') for i in out_lst]
print u'; '.join(out_lst)

with open(outfile, 'w') as f:
    print >>f, u'; '.join(out_lst).encode('utf-8')