What is the ruling on money taken by the questioner from his company with the intention of returning it, but he has not returned it after his repentance? And does the ruling differ if he is unable to return it directly, or if his colleague took money in his name, or if the company delayed in paying his salaries, or breached the end-of-service bonus contract, or is on the verge of bankruptcy?

It is not permissible for an employee entrusted with collecting money to take from it for himself with the intention of returning it, because this is a breach of trust. The money must be returned to the company, and there is no obligation to inform them. As for what your colleague took in your name, he is obligated to return it, unless he took it from the money under your control or you facilitated it for him, in which case you are obligated to return it and then seek reimbursement from him. The company's delay in paying salaries does not permit withholding money. If there was an explicit agreement that the end-of-service benefits would be based on the full salary, then the difference between them is your right, and you may take its equivalent from the money in your possession if you despair of collecting it.