Replace values in selected columns by passing column name of data.frame into apply() or plyr function
df <- data.frame(a=1:5, b=sample(1:5, 5, replace=TRUE), c=5:1)
df
  a b c
1 1 4 5
2 2 3 4
3 3 5 3
4 4 2 2
5 5 1 1

df
  a b  c
1 1 4  NA
2 2 3  4
3 3 NA 3
4 4 2  2
5 5 1  1

var <- c("b", "c")

df <- within(df, sapply(var, function(x) x <- replace(x, x==5, NA)))

df <- data.frame(a=1:5, b=sample(1:5, 5, replace=TRUE), c=5:1)
df
var <- c("b","c")
df[,var] <- sapply(df[,var],function(x) ifelse(x==5,NA,x))
df

df[,var][df[,var] == 5] <- NA