In windows command line you could:
FOR /D /R %g IN (*.gdb) DO ogr2ogr -update -append -f FileGBD D:\output.gdb x:\incoming\%g input_layername
Just place the input_layername after the input dataset.
/D tells FOR to search for directories and /R asks it to do it recursively.
In a .bat file, replace the '%' with '%%', so %g > %%g
Extended batch file example using a) gdb's wrapped in zipfiles as data source, b) projecting to a new coordinate system, and c) selecting multiple input feature classes:
set ogropt=-f FileGBD --config FGDB_BULK_LOAD YES -t_srs EPSG:3579
set layers=Layer_1 Layer_2 Layer_3
for /r %%g in (x:\incoming\*gdb.zip) do (
ogr2ogr %ogropt% -update -append output.gdb %%g %layers%
)
-lco FEATURE_DATASET=NAME? – Nathan W Mar 26 '15 at 23:17