IDAPython script to patch binaries. 
IDAPython: https://code.google.com/p/idapython/
Helfpul if you want to run scripts on startup: https://code.google.com/p/idapython/source/browse/trunk/examples/idapythonrc.py
Alt F7 to load scripts
File > Produce file > Create DIF file
Edit > Patch program > Apply patches to input file
    Shift-N: Convert instruction to nops
    Shift-X: Nop all xrefs to this function
    Shift-J: Invert conditional jump
    Shift-U: Make jump unconditional
    Shift-P: Patch instruction
    Shift-Z: Undo modification (Won't always work. Should still be careful editing.)
    Shift-Y: Redo modification (Won't always work. Should still be careful editing.)
import os
import idaapi
import idc
import re
import Fentanyl
import AssembleForm
import FtlHooks
import CodeCaveFinder
import Util
import Neuter
    from PySide import QtGui
    from PySide import QtCore
except ImportError:
    print "PySide unavailable, no GUI"
    QtCore = None
    QtGui = None
""" Main """
ftl_path = os.path.dirname(__file__)
ftl = Fentanyl.Fentanyl()
asf = AssembleForm.AssembleForm()
ftlh = FtlHooks.FtlHooks()
ftln = Neuter.Neuter(ftl)
#XXX: Store the parents of the QWidgets. Otherwise, some get GCed.
hack = []
#Interfaces to the methods in ftl
def nopout():
    start, end = Util.get_pos()
    ftl.nopout(start, end - start)
import traceback
def assemble():
    try: assemble_()
    except e:
        print traceback.format_exc()
def assemble_():
    success = False
    while not success:
        v = asf.process()
        if not v or not v['inp'].strip(): return
        start, end = Util.get_pos()
        lines = [i.strip() for i in v['inp'].replace(';', '\n').strip().split('\n')]
        success, data = ftl.assemble(start, lines, v['opt_chk']['fixup'], v['opt_chk']['nopout'])
        if not success:
            print data
def togglejump():
    start, end = Util.get_pos()
def uncondjump():
    start, end = Util.get_pos()
def nopxrefs():
    start, end = Util.get_pos()
    func = idaapi.get_func(start)
    if func:
def undo():
    if ftl.undo() is None:
        print "Nothing to undo"
def redo():
    if ftl.redo() is None:
        print "Nothing to redo"
def savefile():
    output_file = AskFile(1, "*", "Output File")
    if not output_file:
#Interface to spelunky
def openspelunky():
    window = CodeCaveFinder.CodeCaveWindow()
def neuter():
#Helper functions
def bind_ctx_menus():
    #Find all the menus we need to modify
    menus = []
    for wid in qta.allWidgets():
        if not isinstance(wid, QtGui.QMenu):
        parent = wid.parent()
        if  parent.__class__ != QtGui.QWidget:
        #Find Hex/IDA Views
        if  'Hex View' in parent.windowTitle() or \
            len(parent.windowTitle()) == 1 \
    #Filter out menus with actions
    menus = [i for i in menus if not i.actions()]
    print 'Bound entries to %s' % menus
    #Insert each entry into the context menu
    for i in range(len(menus)):
        menu = menus[i]
        for qact in qdata:
#Hotkey definitions
hotkeys = [
    ('Replace with nops', True , ['Alt', 'N'], 'nopout.png', nopout),
    ('Nops all Xrefs'   , True , ['Alt', 'X'], 'nopxrefs.png', nopxrefs),
    ('Assemble'         , True , ['Alt', 'P'], 'assemble.png', assemble),
    ('Toggle jump'      , True , ['Alt', 'J'], 'togglejump.png', togglejump),
    ('Force jump'       , True , ['Ctrl', 'Alt', 'F'], 'uncondjump.png', uncondjump),
    ('Undo Patch'       , False, ['Alt', 'Z'], None, undo),
    ('Redo Patch'       , False, ['Alt', 'Y'], None, redo),
    ('Save File'        , False, ['Alt', 'S'], None, savefile),
    ('Find Code Caves'  , False, ['Alt', 'C'], None, openspelunky),
    ('Neuter Binary'    , False, ['Ctrl', 'Alt', 'N'], None, neuter)
#Register hotkeys
for name, in_menu, keys, icon, func in hotkeys:
    idaapi.add_hotkey('-'.join(keys), func)
#Register menu items
if QtCore:
    qta = QtCore.QCoreApplication.instance()
    qdata = []
    for name, in_menu, keys, icon, func in (i for i in hotkeys if i[1]):
        qact = QtGui.QAction(QtGui.QIcon(os.path.join(ftl_path, 'icons', icon)), name, qta)
        qks = QtGui.QKeySequence('+'.join(keys))
#Rebind on new db
ftlh.register('LoadFile', bind_ctx_menus)
#Rebind on new IDA View
ftlh.register('WindowOpen', bind_ctx_menus)
ftlh.register('GraphNewProximityView', bind_ctx_menus)
#Rebind on new Hex View
ftlh.register('ToggleDump', bind_ctx_menus)
#Reset on IDB close
ftlh.register('CloseBase', ftl.clear)