You can modify strip.text.x (or strip.text.y) using theme_text(), for instance
qplot(hwy, cty, data = mpg) +
facet_grid(. ~ manufacturer) +
opts(strip.text.x = theme_text(size = 8, colour = "red", angle = 90))
Update: for ggplot2 version > 0.9.1
qplot(hwy, cty, data = mpg) +
facet_grid(. ~ manufacturer) +
theme(strip.text.x = element_text(size = 8, colour = "red", angle = 90))