#Libraries
library("reshape")
library("data.table")

#Specify list of multiple dataframes
filelist <- list(data.frame(x=c(1,1,1,2,2,2,3,3,3), y=c(1,2,3,1,2,3,1,2,3), a=1:9),
                 data.frame(x=c(1,1,1,2,2,2,3,3,4), y=c(1,2,3,1,2,3,1,2,1), b=seq(from=0, by=5, length.out=9)),
                 data.frame(x=c(1,1,1,2,2,2,3,3,4), y=c(1,2,3,1,2,3,1,2,2), c=seq(from=0, by=10, length.out=9)))

#Merge with merge_recurse()
listMerged <- merge_recurse(filelist, by=c("x","y"))

#Attempt with data.table
ids <- lapply(filelist, function(x) x[,c("x","y")])
unique_keys <- unique(do.call("rbind", ids))
dt <- data.table(filelist)
setkey(dt, c("x","y")) #error here

Reduce(function(x, y) x[y[J(unique_keys)]], filelist)

> listMerged
   x y  a  b  c
1  1 1  1  0  0
2  1 2  2  5 10
3  1 3  3 10 20
4  2 1  4 15 30
5  2 2  5 20 40
6  2 3  6 25 50
7  3 1  7 30 60
8  3 2  8 35 70
9  3 3  9 NA NA
10 4 1 NA 40 NA
11 4 2 NA NA 80