change color of only one bar in ggplot

Option 1: Change color of only one bar. Following Henrick's suggestion, you can create a new variable with NAs for the default color and character strings/factors for non-default colors (the first one happens to be red):

area.color <- c(NA, "withcolor", NA, NA)
plot.sale.bad <- ggplot(data=df.sale, aes(x=area, y=sale, fill=area.color)) +
  geom_bar(stat="identity") +
  xlab(colnames(df.sale)[1]) +
  ylab(colnames(df.sale)[2]) +
  ggtitle("Porównanie sprzedaży") 
plot.sale.bad

Option 2: Find the name of the default dark gray color you like. This is not the default color if you simply remove the scale_fill_manual line in your original code (in that case, you get four different pastels), so I assume you mean the grey color produced by the code chunk just above this paragraph, for those bars where area.color==NA. In that case, you might look at the source code (or args, anyway) for scale_fill_discrete:

> args(scale_fill_discrete)
# function (..., h = c(0, 360) + 15, c = 100, l = 65, h.start = 0, 
#     direction = 1, na.value = "grey50") 
# NULL

The default for na.value is "grey50". So if you wanted to use scale_fill_manual, you could do it like so:

plot.sale.bad <- ggplot(data=df.sale, aes(x=area, y=sale, fill=area)) +
  geom_bar(stat="identity") +
  scale_fill_manual(values=c("grey50", "red", "grey50", "grey50")) +
  xlab(colnames(df.sale)[1]) +
  ylab(colnames(df.sale)[2]) +
  ggtitle("Porównanie sprzedaży") 
plot.sale.bad

If you like having everything in the ggplot call, you can use an ifelse statement within factor() for the fill as shown below.

This also separates the legend into two categories (i.e. highlighted and not highlighted) so that you aren't repeating the values shown on the x axis. This also provides another illustrative dimension to the plot in the legend.

plot.sale.bad2 <- ggplot(data=df.sale,
                         aes(x=area,
                             y=sale,
                             fill=factor(ifelse(area=="Południe","Highlighted","Normal")))) +
  geom_bar(stat="identity") +
  scale_fill_manual(name = "area", values=c("red","grey50")) +
  xlab(colnames(df.sale)[1]) +
  ylab(colnames(df.sale)[2]) +
  ggtitle("Porównanie sprzedaży") 

plot.sale.bad2

If the legend isn't needed you can add show.legend = FALSE to the geom_bar() call to produce the following: