Tile formats: OGC WMTS & Google & Microsoft QuadTree & NASA World Wind
GDAL2Tiles and MapTiles should support generation of the tiles in non-TMS directory structure...
The first candidate is OGC WMTS format (seems to be compatible with standard Google tile naming convension).
Second candidate are "Microsoft QuadTree" tiles known from MapCruncher for native Virtual Earth overlays (Spherical Mercator and QuadTree).
Third candidate are NASA World Wind tiles - so 512x512 Global Geodetic (-p geodetic) tiles with custom tile structure described at the site: http://issues.worldwind.arc.nasa.gov/confluence/download/attachments/394/world+wind+tile+systemt.gif
I summarized details to different tile naming convention for Spherical Mercator here:
http://www.maptiler.org/google-maps-coordinates-tile-bounds-projection/
The new MapTIler available at http://www.maptiler.com/ renders by default WMTS / Google XYZ tiles. This issue is not a problem anymore.
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Mark Gray commented
Please at least add the choice of Google vs. TMS. Your summary of the tile naming conventions is helpful and the interactive map on that page tells me that I want the TMS naming convention (to match OpenStreetMap) but MapTiler is making the other naming convention which is the same for the Zoom and X folder names but different for each Y filename. (MapTiler uses increasing Y values from North to South, I need them increasing from South to North.) It is so promising having all the right tiles generated, but frustrating that they cannot be found and placed on my map because they use a different naming convention! (The generated sample googlemaps.html and openlayers.html work fine though.)