System addon bringing to Blender a Houdini-like saving system. Every save a versioned copy of the current scene moved into the backup folder in the current scene directory.

backup_and_save.py

# System addon bringing to Blender a Houdini-like saving system. Every save a
# versioned copy of the current scene moved into the backup folder in the
# current scene directory.
#
# Install from Blender User Preferences → Add-ons via the Install from File
# button, then tick the checkbox near the Backup and Save add-on. Searching by
# name is useful here. After that, the Backup and Save operation can be found in
# space bar menu. Navigate to Blender User Preferences → File and set Save
# Versions to 0. It disables .blend1 files creation on each save which is a
# backup system itself. No need to use it anymore. Remove the Ctrl S shortcut
# binded to the "Save Blender File" operation.

bl_info = {
    "name": "Backup and Save",
    "description": "Copy current Blender file to the ./backup folder and save.",
    "version": (1, 0),
    "blender": (2, 74, 0),
    "category": "System"
}

import os
import re
import shutil

import bpy

class BackupAndSave(bpy.types.Operator):
    """Copy current Blender file to the ./backup folder and save"""
    bl_idname = "wm.backup_and_save"
    bl_label = "Backup and Save"

    def execute(self, context):
        src_path = bpy.data.filepath

        # If file not exist, perform a normal save.
        if not os.path.exists(src_path):
            bpy.ops.wm.save_mainfile('INVOKE_DEFAULT')
            return {'CANCELLED'}

        # Otherwise, create proper backup path.
        src_file = os.path.basename(src_path)
        src_name, _ = os.path.splitext(src_file)
        src_dir = os.path.dirname(src_path)
        bak_dir = os.path.join(src_dir, "backup")

        # Compute bak number.
        if os.path.exists(bak_dir):
            # Find maximum bak number from existing backups.
            num = 0
            for f in os.listdir(bak_dir):
                if not f.startswith(src_name + "_bak"):
                    continue
                match = re.search(r".*_bak([0-9]+)\.blend", f)
                if not match:
                    continue
                match_num = int(match.group(1))
                num = max(num, match_num)
            bak_num = num + 1
        else:
            os.mkdir(bak_dir)
            bak_num = 1

        bak_file = "{}_bak{}.blend".format(src_name, bak_num)
        bak_path = os.path.join(bak_dir, bak_file)

        # Backup file and save.
        shutil.copy2(src_path, bak_path)
        bpy.ops.wm.save_mainfile()
        return {'FINISHED'}

# store keymaps here to access after registration
addon_keymaps = []

def register():
    bpy.utils.register_class(BackupAndSave)
    # handle the keymap
    wm = bpy.context.window_manager
    km = wm.keyconfigs.addon.keymaps.new(name='Window', space_type='EMPTY')
    kmi = km.keymap_items.new(BackupAndSave.bl_idname, 'S', 'PRESS', ctrl=True)
    addon_keymaps.append(km)

def unregister():
    bpy.utils.unregister_class(BackupAndSave)
    # handle the keymap
    wm = bpy.context.window_manager
    for km in addon_keymaps:
        wm.keyconfigs.addon.keymaps.remove(km)
    addon_keymaps.clear()

if __name__ == "__main__":
    register()