different colors for each bar in stacked bar graph - base graphics

This works by adding one coloured bar to the plot at a time:

# white bars 
barplot(x, col='white', axes=F, axisnames=F, yaxp=c(0,1,2), las=1)
cols=c('grey','red','green')

# add coloured bars
for (i in 1:ncol(x)){
    xx = x
    xx[,-i] <- NA
    colnames(xx)[-i] <- NA
    barplot(xx,col=c('white',cols[i]), add=T, axes=F) 
}

library(ggplot2)
library(reshape2)
x <- data.frame(aa=c(0.2,0.6,0.1,0.1),
                bb=c(0.4,0.5,0.05,0.05),
                cc=c(0.5,0.25,0.1,0.15),
                dd = 1:4)
x <- melt(x, "dd")
col=c(rep(c("white","grey"),2),rep(c("white","red"),2),rep(c("white","green"),2))
ggplot(x, aes(x = variable, y = value)) + geom_bar(stat = "identity", fill = col)

A workaround: extend your matrix so that values correspond to fictitious categories, with just one color per category. Only one of aa, bb and cc will actually have data in those categories.

xx <- rep(0,4)
x <- matrix(c(aa,xx,xx,xx,bb,xx,xx,xx,cc),ncol=3)
x
      [,1] [,2] [,3]
 [1,]  0.2 0.00 0.00
 [2,]  0.6 0.00 0.00
 [3,]  0.1 0.00 0.00
 [4,]  0.1 0.00 0.00
 [5,]  0.0 0.40 0.00
 [6,]  0.0 0.50 0.00
 [7,]  0.0 0.05 0.00
 [8,]  0.0 0.05 0.00
 [9,]  0.0 0.00 0.50
[10,]  0.0 0.00 0.25
[11,]  0.0 0.00 0.10
[12,]  0.0 0.00 0.15

And plot as you did:

col <- c(rep(c("white","grey"),2),rep(c("white","red"),2),rep(c("white","green"),2))
barplot(x,col=col)