It's harder to replicate the functionality of Eterm, though the aterm program is similar in intent and effect. Both E and Eterm use themes. Themes are eye candy, rarely useful in practice. I find them useful for Eterm, but for E I don't use themes for programming support. The most important modification I made to E was to change the default keybindings with the e16keyedit program.
E can remember a program's location and command line invocation.
This means that if a program has a unique name, E can restart it the next time you login, or just remember its position for the next time you start it. The name is the X name of the window, usually specified with the -name parameter to the program. Eterm uses themes to specify custom behavior. I find a transparent Eterm, set to stick in the layer below all other windows, to be very useful in everyday work. It's always available because it's sticky, it never obscures other windows, and provides nice visual relief from black and white.