class MainWindow(QtGui.QMainWindow):
    def __init__(self):
        super(MainWindow, self).__init__()
        self.MainNote = Note('main', 'undef', None)

    def dump(self):
        f=open(self.workdir+"\\Notes\\" + self.getUser(),"wb")
        pickle.dump(self.MainNote,f)  #сохраняю объект, в ктором есть ссылки
        f.close()


class Note():
    ChildrenList = [] #список ссылок

    def __init__(self, notename, user, parent):
        self.Name = str(notename)
        self.User = str(user)
        self.Text = self.Name + self.NewNoteTip
        self.Parent = parent

        ChildrenList = []

    def addChildNote(self,notename):
        childNote=Note(notename,self.User,self) 
        self.ChildrenList.append(childNote)  # добавляется ссылка на объект
        return childNote

    def childs(self):
        return self.ChildrenList

    def getNoteByName(self,notename):
        notename = str(notename)
        if self.name() == notename:
            return self
        for x in self.childs():  # здесь возникает проблема: так как в списке есть и сам объект возникает бесконечная рекурсия (и много других проблем в разных частях кода).
            childRes = x.getNoteByName(notename)
            if childRes != None:
                return childRes
            else:
                return None
        return None

import pickle
class A():
    ref = []
    def __init__(self):
        self.ref.append(B())
    
class B():
    int = 10
    def __init__(self):
        self.int = 99
    
if __name__ == '__main__':
    test = A()
    f = open('test','wb')
    pickle.dump(test,f)
    f.close()
    print(test.ref[0].int)
    del test
    f=open('test','rb')
    test = pickle.load(f)
    f.close()
    print(test.ref[0].int)

class Note():
    Text = ''
    NewNoteTip = "\n\nDescribe here your note"
    Name = ""
    ChildrenList = []
    User = ""
    Parent = None
    
    def __init__(self, notename, user, parent):
        self.Name = str(notename)
        self.User = str(user)
        self.Text = self.Name + self.NewNoteTip
        if parent != None:
            self.Parent = parent
        else:
            self.Parent = self
        self.ChildrenList = []

    def note(self):
        return self.Text

    def save(self, text):
        self.Text = str(text)

    def name(self):
        return self.Name

    def addChildNote(self,notename):
        childNote=Note(notename,self.User,self)
        self.ChildrenList.append(childNote)
        return childNote

    def delNote(self,note):
        self.ChildrenList.remove(note)

    def childs(self):
        return self.ChildrenList

    def getNoteByName(self,notename):
        notename = str(notename)
        if self.name() == notename:
            return self
        for x in self.childs():
            childRes = x.getNoteByName(notename)
            if childRes != None:
                return childRes
            else:
                return None
        return None

    def parent(self):
        return self.Parent

note = Note("MainNote", "user", None)
note.addChildNote("ChildNote")
f = open('test.pickle','wb')
pickle.dump(note, f)
f.close()
print "Before:", note.Name, note.childs()[0].Name
del note
f=open('test.pickle','rb')
note = pickle.load(f)
f.close()
print "After:", note.Name, note.childs()[0].Name