The two had a very positive relationship, and Gloria was clearly a good influence on Nicholas. After her death he began a spiral that made him the hard, self-obsessed man that he is. He is angry at himself for escaping her long illness by throwing himself into his work on the Ninth Chevron Project.
Gloria appeared to Nicholas in a lucid dream state, helping him to uncover vital information about accessing Destiny's control systems. She may even have been a subconscious manifestation of the ship itself. Some months later, when Rush found the ship's bridge, she appeared to him multiple times there -- though he was unsure if she is an attempt by the ship to communicate, or a symptom of his own fractured psyche.
Human - Within a lucid dream caused by Destiny, Rush is forced to relive the horrible events of his wife's slow death from cancer, and confront the person it has made him.
Aftermath - After Nicholas discovers Destiny's bridge, he sees Gloria there -- and is not sure if she is the ship communicating with him or an hallucination of his own subconscious.
Awakening - On the bridge, the vision of Gloria continues to question Nicholas' actions.
Pathogen - Rush continues to see Gloria on the ship, expressing concern over how hard he is pushing himself, and the lives that his carelessness has cost so far.