Do not want scientific notation on plot axis

Use options(scipen=5) or some other high enough number. The scipen option determines how likely R is to switch to scientific notation, the higher the value the less likely it is to switch. Set the option before making your plot, if it still has scientific notation, set it to a higher number.

You can use format or formatC to, ahem, format your axis labels.

For whole numbers, try

x <- 10 ^ (1:10)
format(x, scientific = FALSE)
formatC(x, digits = 0, format = "f")

If the numbers are convertable to actual integers (i.e., not too big), you can also use

formatC(x, format = "d")

How you get the labels onto your axis depends upon the plotting system that you are using.

Try this. I purposely broke out various parts so you can move things around.

library(sfsmisc)

#Generate the data
x <- 1:100000
y <- 1:100000

#Setup the plot area
par(pty="m", plt=c(0.1, 1, 0.1, 1), omd=c(0.1,0.9,0.1,0.9))

#Plot a blank graph without completing the x or y axis
plot(x, y, type = "n", xaxt = "n", yaxt="n", xlab="", ylab="", log = "x", col="blue")
mtext(side=3, text="Test Plot", line=1.2, cex=1.5)

#Complete the x axis
eaxis(1, padj=-0.5, cex.axis=0.8)
mtext(side=1, text="x", line=2.5)

#Complete the y axis and add the grid
aty <- seq(par("yaxp")[1], par("yaxp")[2], (par("yaxp")[2] - par("yaxp")[1])/par("yaxp")[3])
axis(2, at=aty, labels=format(aty, scientific=FALSE), hadj=0.9, cex.axis=0.8, las=2)
mtext(side=2, text="y", line=4.5)
grid()

#Add the line last so it will be on top of the grid
lines(x, y, col="blue")

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))