Sometimes (eg. doing it for a bulk of geodatasets) converting and transforming geodatasets from their Source-CRS to another with command line tools like ogr2ogr (http://www.gdal.org/ ) can be helpful.
With ogr2ogr it’s also an easy task to use NTv2-based transformations like for Austria the AT_GIS_GRID.
One of the most precise and best ways to transform geodata from the Austrian MGI-System to ETRS89 is using the AT_GIS_GRID (NTv2 Transformation) provided by the BEV. Thanks to the developers of the NTV2-PlugIn for QGIS it is really easy to use now.
Das NTv2-basierende Transformationsverfahren vom österr. Bundesmeldenetz (BMN / MGI) nach ETRS89 (und auch WGS84) ist nun auch mit den österr. Parametern des BEV (AT_GIS_GRID) in ArcGIS 10.2 “implementiert” – allerdings mit einem kleinem manuellen Eingriff.