Many thanks to Beverly Wolfe ("Lurker since 1997") for providing the following details about this film:

For the movie's first Joni reference, Meg Ryan's character, Kathleen Kelly, is alone and reminiscing about her mother while decorating a Christmas tree in the window of her lonely children's bookstore [The Shop Around The Corner].

It's shortly before Christmas, and big, bad Fox Books, owned by Tom Hanks' character, Joe Fox, is taking away all her business. The otherwise upbeat Kathleen is beginning to feel there is no hope. As snow gently falls outside the shop, she sits beside the Christmas tree and watches people walk by with shopping bags brimming with purchases from Fox Books. Kathleen speaks the opening lines to River and says:

KATHLEEN: It's coming on Christmas, they're cutting down trees. Do you know that Joni Mitchell song? "I wish I had a river I could skate away on?" It's such a sad song, and not really about Christmas at all, but I was thinking about it tonight as I was decorating my Christmas tree and unwrapping funky ornaments made of Popsicle sticks, and missing my mother so much I almost couldn't breathe.
Watch Scene HERE

Later on in the movie, Kathleen's little children's book store closes because of competition from Fox Books, and Joe Fox attempts to mend their relationship. While strolling through the streets of New York City, Kathleen mentions that she could never date a man who owns a boat. (Unbeknownst to her, Joe owns a boat. What's more, he's also aware of the fact that she's a Joni Mitchell fan, although due to the plot line, Kathleen doesn't know this.) So, not to be outdone, Joe says:

JOE: I could never be with someone who likes Joni Mitchell. "It's cloud illusions I recall, I really don't know clouds at all." What does that mean? Is she a pilot? Is she taking flying lessons? It must be a metaphor for something, but I don't know what it is.
Watch Scene HERE at 08:09

(Contributed by Ilaria, Beverly Wolfe)