E.g. when moving the workspace browser to the right toolbar, that position should be remembered on the next run. Note: What about (semi-accidentally) removed tool windows? Will casual users be able to figure out, how to restore these?
Perhaps creating a configuration file somewhere with all the appearance settings would be simple solution.
While working on related parts of the code, I found out that we already do this ;) But the implementation is not good, yet. What happens is that regular windows and tool windows are treated alike: Their position is saved / restored with the workspace (by default). Thus, if you move a tool window, save the workspace, then in the next session load the workspace, the tool window will be at the new position. I guess it probably makes more sense to always save / restore tool window position when quitting / starting a session. Or this could be a separate configuration item. Will have to think a bit about what is best. See also: Settings->General->Workspace layout
Rkward should remember not only toolbar positions but should also remember positions and or the detachment status (whether "detached") of opened windows. Also it should remember whether it should display the "R console" at startup instead of the regular welcome note.