Why does it say "Nora'os Nifleisi"?
Radak: There are awesome deeds in the creation of me, and I thank You for them. Chachamim recognize the wonders of man's formation. Every limb was created for a need. Everyone must contemplate them, and amidst this recognize His wonders and thank for them.
Malbim: After saying that Hashgachah Pratis hovers over man in all his individual deeds, it says that due to the wonders of his deeds, he has this Hashgachah more than all other creations. The two ends of the creation - spiritual and physical, Shamayim and Eretz, are separate in all their matters. This is spiritual, and this is physical. This is simple, and this is composite; in this, the individuals last, and in this, the species endures. This is at the height of the world, and this is in the depths. One could err to think that different craftsmen made them! Amidst Hashem's Chachmah, He made one being that pertains to both of them. Man's body pertains to the lower world, and his Neshamah pertains to spiritual Bnei Elohim. Via this, Hashem 'signed' that one Creator made both.
Why does it say "Nifla'im Ma'asecha"?
Malbim: Some craftsmen make wondrous designs in silver and gold. These metals are proper to receive fine forms. The craftsman's Chachmah is not recognized through this. Another craftsman makes such designs in iron and rock. Their nature is not to receive such forms. The latter Kli is more esteemed regarding the worker's Chachmah. Similarly, the wondrous forms in man's Nefesh, which is spiritual and apt to get such forms, does not show the Maker's Chachmah, but the Nefesh itself is very dear. Hashem made such forms in the physical body of flesh and bones. The body itself is not so esteemed, but it shows its Maker's Chachmah.
Why does it say "v'Nafshi Yoda'as Me'od"?
Radak: "Me'od" refers to "Nifla'im Ma'asecha." Your deeds are very wondrous, and my Nefesh knows, i.e. my intellectual Nefesh. Even though Your deeds are wondrous in other living beings, none of them recognize this. You put in me an intellectual Nefesh that knows Your deeds and thanks You for them.
Malbim: My Nefesh know that even though it does not show the Maker's Chachmah (refer to 139:14:2:1), it itself is very wondrous, for it is spiritual and very hidden.