Or, just pmin
.
my.dt <- as.data.table(my.df)
system.time(my.dt[,row.min:=pmin(A,B,C)])
# user system elapsed
# 0.02 0.00 0.01
head(my.dt)
# A B C row.min
# [1,] 2 5 2 2
# [2,] 4 5 5 4
# [3,] 1 5 3 1
# [4,] 4 4 3 3
# [5,] 3 5 5 3
# [6,] 1 5 3 1