NEW 5/2014: alternative web-based tool
Tool is java-application, double-click jar-package. Or: rigth-click -> Open with... -> Java (TM) Platform SE Binary. Or use exe-file.
GPSseurantaCalibrationTool2a2.jar (2014-05-17)
GPSseurantaCalibrationTool2a2.exe (2014-05-17)
Calibration output, so called "calibration string", is updated in the bottom of the window and can be copied from there.
Three calibration points are placed by clicking and dragging points on the map with the mouse's RIGHT button. Clicking the map with mouse-right will take nearest (1,2 or 3) calibration point to that location.
Calibration points coordinates can be imported from a few internet map services. Click "Import Lon/Lat" and paste text according instructions:
Right-click place on map, select last item "What's here?" (FIN: Mitä täällä on?) from pop-up menu and copy "62.286712,25.693306" -styled text from google's search textfield.
Note: Google's aerial photos are not very accurately georeferenced.

Double-click the location, from the lower-right corner of map click "Permalink" (FIN: Ikilinkki) and copy url from brower's address bar

Click (to center the map) to location and copy "N 6906796 E 432207" -styled coordinates from upper-right corner of the page: "ETRS-TM35FIN -tasokoordinaatit"

Zoom to desired area, choose GPS-tool in bottom and click desired point. Then copy "62.286712, 25.693306" -styled text.

Use point-tool and copy POINT(247576.625 6616433.75) –styled text from right panel.
Navigate to location and right-click. Then copy "N: 6572876 E: 436475" -styled text from pop-up.
Right-click place on map, copy "WGS 84 (long/lat) 7.87206, 47.10991" -styled figures from WGS 84-line on the Position-popup.

It's possible to import gps-tracks in GPSseuranta- and gpx -file formats. Tracks are automatically drawn according to current calibration. It's also possible to make a "test track" by bringing coorninates from internet map services. Paste one point in a line as one of the formats described above.
To take coordinates from imported track for calibration move upper slider ("point from selected track") to desired point and grab coordinates for calibration point 1, 2 or 3.
Also SHIFT+ left-click on the map moves slider to nearest point of selected track.
To determine hidden areas, check "Hide areas -> add point" -checkbox and click area's corner points with mouse's right button.
When areas are ready their data can be exported. Before that map must be calibrated, because transformation from map point to WGS-coordinates is depenedent on used calibration.
After overall calibration is made, it's possible to make local fixes (if map is not accurate). Fix is determined with base line, shift, inner radius and outer radius.
All points which are (after overall calibration) within inner radius away for base line are moved with shift. Points which are more than inner radius but less than inner radius + outer radius away are moved less so that points inner radius + outer radius/2 away are moved shift/2 etc.
Base line and shift are made by dragging with mouse-right, inner and outer radius are determinated with sliders.