For security of ECC, the choice of the irreducible polynomial is unimportant, because all finite fields with the same cardinal are isomorphic to each other (and the isomorphisms are easy to compute); this is why we can say "the finite field $GF(2^{163})$" even though there are many irreducible polynomials of degree $163$ over $GF(2)$. So the algebraic structure of an elliptic curve is not impacted by the actual field choice (of course, the curve is described with an equation $Y^2+XY=X^3+aX^2+b$ for two given constants $a$ and $b$, and those constants are represented with a given choice for the field; but using another field and applying the isomorphism on $a$ and $b$ yields another curve with the same structure). In practice, we use polynomials which promote implementation efficiency, i.e. polynomials with very low Hamming weight ($3$ if possible, $5$ otherwise), and where the non-zero coefficients are of the smallest possible degree (to make post-multiplication modular reduction easier).
For the Rijndael S-Box, things are not as simple. In the original Rijndael specification, there are some explanations on the design rationale, which were not copied into the final FIPS 197 standard. The S-Box is treated page 26; the use of an inverse in $GF(2^8)$ comes from a 1994 article by Nyberg, as providing good defense against differential cryptanalysis. To this inverse, Daemen and Rijmen added the so-called "affine mapping" which is meant to mask the algebraic structure of the said multiplicative inverse. All details are not given, so presumably they tried many polynomials (there are 30 irreducible polynomials of degree 8 over $GF(2)$, 16 of which being primitive) and many possible affine mappings, "measured" resistance to differential and linear cryptanalysis, and kept the best candidate.
Daemen and Rijmen published a book on the design of Rijndael (I have not read it).
