Here is how you can change the colour of the box-and-whiskers, and also the overlaid points.

Note the pairings for the colouring:

• Box-and-whisker plot: geom_boxplot() and scale_fill_manual()
• Scatter plot: geom_jitter() and scale_color_manual()

.

df <- data.frame(
  Group = c(rep('B-cell\nlymphocytes',50), rep('Natural\nkiller cells', 50)),
  log2(matrix(rexp(200, rate=.1), ncol=2)))
colnames(df) <- c('Group', 'Gene1', 'Gene2')

require(reshape2)
require(ggplot2)

df <- melt(df, id.vars = c('Group'))
colnames(df) <- c('Group', 'Gene', 'Expression')

ggplot(data = df, aes(x = Group, y = Expression)) +

    geom_boxplot(
      position = position_dodge(width=0.5),
      outlier.shape = 17,
      outlier.colour = 'red2',
      outlier.size = 0.1,
      aes(fill = Group)) +
    scale_fill_manual(values = c( 'red', 'royalblue')) + # for boxplot

    #Add the scatter points (treats outliers same as 'inliers')
    geom_jitter(
      position = position_jitter(width = 0.3),
      size = 3.0,
      aes(colour = Group)) +
    scale_color_manual(values = c('pink', 'skyblue')) + # for scatter plot dots

    # facet by Gene
    facet_wrap(~ Gene, ncol = 2) +

    #Set the size of the plotting window
    theme_bw(base_size=24) +

      #Modify various aspects of the plot text and legend
      theme(
        legend.position = 'none',
        legend.background = element_rect(),
        plot.title = element_text(angle = 0, size = 16, face = 'bold', vjust = 1),
        plot.subtitle = element_text(angle = 0, size = 16, face = 'bold', vjust = 1),
        plot.caption = element_text(angle = 0, size = 16, face = 'bold', vjust = 1),

        axis.text.x = element_text(angle = 45, size = 16, face = 'bold', hjust = 1.10),
        axis.text.y = element_text(angle = 0, size = 16, face = 'bold', vjust = 0.5),
        axis.title = element_text(size = 16, face = 'bold'),
        axis.title.x = element_text(size = 16, face = 'bold'),
        axis.title.y = element_text(size = 16, face = 'bold'),

        #Legend
        legend.key = element_blank(),       #removes the border
        legend.key.size = unit(1, 'cm'),        #Sets overall area/size of the legend
        legend.text = element_text(size = 14, face = 'bold'),   #Text size
        title=element_text(size = 14, face = 'bold'),

        #facet wrap
        strip.text.x = element_text(size = 14, face = 'bold'),
        strip.text.y = element_text(size = 14, face = 'bold', angle=0),
        strip.background = element_rect(fill = 'white'), 
        strip.text = element_text(size = 14, face = 'bold', colour = 'black'))+

    #Change the size of the icons/symbols in the legend
    guides(colour = guide_legend(override.aes = list(size = 2.5))) +

    #Set x- and y-axes labels
    xlab('Immune cell class') +
    ylab('Expression') +

    labs(title = 'Good morning',
      subtitle = 'Guten morgen',
      caption = 'Buongiorno')

Kevin