I don't believe there is a built-in function for this. The best you could try is something like:
lsts <- lapply(1:5, function(x) sample(letters, 10)) # make some data (see below)
maxcomb <- which.max(apply(combs <- combn(length(lsts), 2), 2,
function(ix) length(intersect(lsts[[ix[1]]], lsts[[ix[2]]]))))
lsts <- lsts[combs[, maxcomb]]
# [[1]]
# [1] "m" "v" "x" "d" "a" "g" "r" "b" "s" "t"
# [[2]]
# [1] "w" "v" "t" "i" "d" "p" "l" "e" "s" "x"
A dump of the original:
[[1]]
[1] "z" "r" "j" "h" "e" "m" "w" "u" "q" "f"
[[2]]
[1] "m" "v" "x" "d" "a" "g" "r" "b" "s" "t"
[[3]]
[1] "w" "v" "t" "i" "d" "p" "l" "e" "s" "x"
[[4]]
[1] "c" "o" "t" "j" "d" "g" "u" "k" "w" "h"
[[5]]
[1] "f" "g" "q" "y" "d" "e" "n" "s" "w" "i"