You can actually use plyr's rename function as part of dplyr chains. I think every function that a) takes a data.frame as the first argument and b) returns a data.frame works for chaining. Here is an example:
library('plyr')
library('dplyr')
DF = data.frame(var=1:5)
DF %>%
# `rename` from `plyr`
rename(c('var'='x')) %>%
# `mutate` from `dplyr` (note order in which libraries are loaded)
mutate(x.sq=x^2)
# x x.sq
# 1 1 1
# 2 2 4
# 3 3 9
# 4 4 16
# 5 5 25
UPDATE: The current version of dplyr supports renaming directly as part of the select function (see Romain Francois post above). The general statement about using non-dplyr functions as part of dplyr chains is still valid though and rename is an interesting example.