The next appearance of the tennis ball is in the season finale of season one (Identity). Wilfred gets ran over and doesn't remember Ryan when he wakes up. Ryan runs to his house in search of Wilfred's will in his basement but finds a closet instead. He is staring at it when the tennis ball rolls to his feet. He is still staring at this ball in the first episode of season two.
In Answers, when Ryan is hallucinating that Wilfred is really a normal man wearing a dog suit while everyone in his life is in on it, tennis balls are spotted with the human Wilfred's possessions.
While Wilfred is dying of lung cancer (Resistance), Ryan is pulled into a dream in which he is playing catch with Wilfred with the tennis ball. It is their final goodbye scene with Wilfred as a live dog. At the end of the episode, Ryan is convinced human in a dog suit Wilfred was his imagination and in a fit of anger throws the tennis ball into the ocean.
Ryan is finally reunited with the ball in the series finale Happiness when he is sitting on the beach with Wilfred once more and sees it wash up onshore.