If you can stand to export them as PDF, use Adobe Photoshop (PS) /Photoshop Elements (PSE) to overlay them. The result can be saved as a multi-layer pdf with markups. Tools within PS make it easy to nudge moved views, check views that are moved to other sheets, and find even single character changes in notes. I've remarked on the method on this site, if you care to search for it.
Since it works with anything available in a PDF or bitmap, it can be used to compare scanned drawings to CAD generated ones.
I've tried GIMP for this purpose, but GIMP is slow enough that the price of PSE is more than worthwhile.
Creo View MCAD may work for this, though I haven't seen any vector based markups handle views and other objects that can move on a page or to other pages. If comparing is all you need, Creo View MCAD looks like a steamshovel for digging a flower bed. Obviously it is much more capable for non-comparison purposes.