I found this
thread on google, which discusses the relative merits of scientific plotting software in linux. The poster highly recommends a combination of
gnumeric (a gnome-based spreadsheet, that my accountant wife says is comparable to Excel XP) and
guppi (gnome-based scientific plotting tool).
The guppi project page also has
links to other scientific plotting software.
You may also want to check out
SciGraphica, another GPL scientific plotting package.