You will not have to use 'continue'. You should have your functions under the 'if' statement (since you want to project all shapefiles with an Unknown coordinate system), and 'pass' under your 'else' statement. Pass will skip the shapefiles that have a coordinate system defined:
if sr.name == "Unknown":
# Determine the new output feature class path and name
outFeatureClass = os.path.join(outWorkspace, infc.strip(".shp"))
# Set output coordinate system
outCS = "Coordinate Systems\Geographic Coordinate Systems\World\WGS 1984.prj"
outCS2 = "Coordinate Systems\Projected Coordinate Systems\World\Cylindrical Equal Area (world).prj"
arcpy.DefineProjection_management(infc, outCS)
arcpy.Project_management(infc, outFeatureClass, outCS2)
arcpy.AddMessage("The shapefiiles have been reprojected")
print "Get Area Info...."
else:
pass