Calbur vs Energy Based Clustering

The biggest difference is in philosophy. (And which to choose would depend on what you're interested in doing with the clusters centers downstream.)

Calibur clustering is purely a structural based one. It doesn't take energy into account at all. The cluster centers are those structures which are structurally closest to the average structure of the cluster. It'll give you structural representatives.

The energy-based clustering is more a filtering mechanism. It prefer the low-energy structures, and then filters out structures which are "practically identical" to those low energy structures. The cluster centers are low energy structures, but "different enough" from each other.

So which to use depends on why you want to use clustering. Often why you're performing clustering is to reduce the redundancy in output. (There's not really a point in taking two structures which are 0.2 Ang rmsd both forward. One is representative enough of that structural region.) In that sort of case, you're probably better off with the energy-based approach, as it takes forward the "best" structure (by Rosetta energy), but reduces the structural ensemble to a point where each is "different enough" from each other.

Calibur is more suited for a standard final-analysis  clustering approach, where getting the structural representative (independent of score) is the goal.  (But if you're then going to analyze the energy of the cluster centers, you still might want the energy-based one.) Calibur is also a more conventional clustering approach (whereas energy-based clustering is not a common clustering technique), so reviewers are likely to be more familiar with it.