Finding the largest set of points of limited diameter
There's an $O(n^3\log n)$ time algorithm for the two-dimensional version of this problem in my paper with Jeff Erickson, "Iterated nearest neighbors and finding minimal polytopes", Disc. Comp. Geom. 11:321-350, 1994. Actually the paper primarily looks at the dual problem: given the number of points in the subset, find the smallest possible diameter; but it uses the problem you describe as a subroutine. At least at the time we wrote it, we didn't know anything subexponential for higher dimensions (although if the subset has only $k$ points in it the exponential part can be made dependent on $k$ rather than $n$ using techniques in the same paper).