Is your ArcReader project basically a view only application? If so (and if you have ArcGIS Server), might you consider creating a FlexViewer application to replace ArcReader. There are many configurable FlexViewer widgets that don't require any programming that would make this a fairly simple and straight forward process. This would remove the dependency of having to install ArcReader software on client machines (Not sure how big of a deal this is to you).
You might also consider AGOL, but it currently has some labeling deficiencies that might make it more difficult to duplicate your current ArcReader project.