In a nucleus, the neutrons and protons can arrange themselves in a variety of way - there are different energy levels available to them. One of them is the ground state, the lowest energy arrangement of the nucleons. But, as gamma transitions show, there are excited energy levels as well. Such transitions have been mapped in various ways, and results can be found at, for example, ENSDF and TUNL.
Now, your plots above are likely plots of the total neutron cross section on various nuclei. The total cross section is comprised of some number (sometimes quite large) of different possible scattering processes. Each process will have its own cross section, determined by the incoming neutron's interaction with the nucleus, and oftentimes specific (excited) nuclear energy levels.
Lets take the $^{11}$B(n,g)$^{12}$B reaction. With a neutron coming in, and only a gamma going out, it is pretty hard to conserve both energy and momentum (since photon momentum is pretty small you only have a narrow window available to match them up). Now, if we look at an energy level diagram (from TUNL), you see (just for 12B):
One sees, on the left (ignore the slanted line which is $\beta$- decay from 12Be) the energy of $^{11}$B plus a neutron. It does not line up exactly with an energy level in the $^{12}$B diagram, but there are a variety of levels above it.
Now turn to the ENDF data for neutrons on $^{11}$B, with blue the total cross section and green the $^{11}$B(n,g)$^{12}$B cross section. (Note there are another 20 odd different reactions with data in the ENDF data base.
For that specific reaction, you can start lining up the $^{12}$B energy levels, minus the 3.370MeV where $^{11}$B+n lies, and see that the peaks in the $^{11}$B(n,g)$^{12}$B cross section correspond to allowed nuclear energy levels in $^{12}$B. This should not be surprising from, say, Fermi's golden rule - if there is no allowable final state (e.g. $^{12}$B nuclear state) there is no way for the reaction/scattering to take place.
So, all those messy peaks are various resonant scattering events. Exactly what they are can be determined by digging deeper into the data, such as plotting up various specific reaction cross sections. But they will all relate back to various excited nuclear states in the compound nucleus.