Most (but not all) Siddurim have the פסוק of ויהי נועם at the end of הנני מוכןs (such as before ספירת העומר, before the ארבע כוסות, or before בדיקת חמץ).
Where does this practice come from and why is it done?
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The pasuk of ויהי נועם concludes, not the הנני מוכן exactly, but more specifically, the paragraph of לשם יחוד. This paragraph states intent to perform the mitzvot in conjunction with uniting the Holy One, blessed be He, and His Sh'china. This is a Kabbalistic declaration, in accord with the customs of the Ari.
I'm certainly not qualified to answer Kabbalah questions, so I don't know the reason for concluding that paragraph with ויהי נועם.
In Sephardic congregations, there is a similar paragraph before Shacharit, Mincha, and Arvit, as well as before Birkat HaMazon and other mitzvot.