I regularly do all kinds of scatter plots in R using the plot command.
Sometimes both, sometimes only one of the plot axes is labelled in scientific not
You can use the axis() command for that, eg :
x <- 1:100000
y <- 1:100000
marks <- c(0,20000,40000,60000,80000,100000)
plot(x,y,log="x",yaxt="n",type="l")
axis(2,at=marks,labels=marks)
gives :

EDIT : if you want to have all of them in the same format, you can use the solution of @Richie to get them :
x <- 1:100000
y <- 1:100000
format(y,scientific=FALSE)
plot(x,y,log="x",yaxt="n",type="l")
axis(2,at=marks,labels=format(marks,scientific=FALSE))