How to select the most representative pathways from a gene enrichment analysis?
This sounds like something that might be amenable to a clustered heatmap plot, or a correlation matrix plot, or something similar. Have you looked at a correlation matrix of the dice coefficient matrix (or maybe just a heatmap plot of that matrix without the correlation matrix)?

The corrplot package looks like it might be useful, in particular the hclust / drawing rectangles presentation.

I can't vouch for this package though; it's just something I found by a search for "R plot correlation matrix".