I'm putting this is the modding forum because it can relate to modding. Many players, whether they mod or not, will "photoshop" their femsheps in various ways. Mr. Vakarian's Noir series is a great example of this. Other great examples populate the "
photomanipulation" section at the femShep deviant Art site. To this end there are several programs used to manipulate photos, the most famous being Photoshop, however it is very pricey.
Here is a list of free or inexpensive photo editing software
Gimp: The most popular free photo editing software on the net.
GIMPShop: It's GIMP w/ a Photoshop GUI.
Paint.NET: To be honest, I don't know much about it, but it has a Photoshop-esque GUI and layers.
Art Rage 2: Has a unique style and is devoted primarily to painting effects. $20.00 for full version.
PaintShop Pro: Once called "The poor man's Photoshop", PSP now has features that PS lacks. $100.00 for full version.
Inkscape: Emulates the vector art of Illustrator for free. Great for making Insignia, avatars, etc.
If you know of more, please post them here. Thanks!