The most obvious point of both comparison and contrast between these two works is that Christopher Marlowe's "The Passionate Shepherd to His Love" is an invitation while Sir Walter Raleigh's "The Nymph's Rely to the Shepherd" is an answer to the proposal. By their very nature, then, they are both connected and nothing alike. While they both clearly reference some of the same images, both poems have different functions: one poses a question and one answers it.
Another obvious point of contrast for these poems is the speaker's tone--as well as the speakers themselves. Marlowe's speaker is a young shepherd who wants the woman he loves to marry him; Marlowe's speaker is that young woman who gives the shepherd her answer. The tone of the "passionate shepherd" is hopeful and romantic; he offers this woman everything he has which is of value (to him, anyway) and promises her a life of pastoral luxury. The tone of the "reply" is, well, not as romantic.
The shepherd highlights some things he hopes will move this woman to marry him, including these:
And I will make thee beds of Roses
And a thousand fragrant posies,
A cap of flowers, and a kirtle
Embroidered all with leaves of Myrtle;
A gown made of the finest wool
Which from our pretty Lambs we pull;
Fair lined slippers for the cold,
With buckles of the purest gold;
A belt of straw and Ivy buds,
With Coral clasps and Amber studs:
The young and hopeful shepherd describes how they will spend their days outdoors, listening to his shepherds play their songs and enjoying the various kinds of beauty found in nature.
Unfortunately, the response is not what the shepherd wanted to hear, "Passionate Shepherd" is full of innocence and delight, while "Reply" is full of skepticism and doubt. It is a contrast between innocence and experience, and experience wins the day. Perhaps there was a time when the nymph might have said yes, but she has lived through a few seasons and knows what happens over time. The nymph points out that everything he offers her is great--until the weather changes, which of course it will, and unless he is lying. Then things will look a little differently:
Thy gowns, thy shoes, thy beds of Roses,
Thy cap, thy kirtle, and thy posies
Soon break, soon wither, soon forgotten:
In folly ripe, in reason rotten.
Thy belt of straw and Ivy buds,
The Coral clasps and amber studs,
All these in me no means can move
To come to thee and be thy love.
All of those lovely things are only temporal, and when the seasons change, they will no longer be beautiful or valuable, at least not to her.
On the other hand, the two poems are quite similar because the "reply" is a mirror, or perhaps an older, wiser echo of the proposal poem. Notice the two quotes from the poem, above, in which the nymph repeats all of the things he said he will give her. This is true for everything in the shepherd's poem. If he mentions sitting on a rock, the reply also mentions it; if he mentions listening to madrigals, so does she. This is really the one thing they have in common, and it is quite significant. There is no mistaking that "Reply" is connected to and a direct response to "Passionate Shepherd."
Despite their containing most of the same elements, it is the tone which most sets these two poems apart. One reflects the innocence and hopefulness of young love while the other expresses the more cynical view that shepherds do not always tell the truth and that seasons will inevitably change.