Similiar problems for me.
here is the query ArcCatalog issues (with a little editing from me for clarification purposes).
I've just installed Apex 4.0 and many (tho not all) my APEX obects are showing.
so the APEX 4.0 schema would be apex_0400000 and APEX 3.2 schema is apex_030200.. both of these aren't filtered out with this query. I think you have to go back to APEX 3 where it was called "FLOWS_030000" (AC.owner != 'FLOWS_030000') for it not to show.
there should be a way to modify ugly piece of hardcoding.
SELECT AC.owner, AC.table_name
FROM ALL_CATALOG AC
WHERE
AC.owner != 'MTSSYS' AND
AC.owner != 'SYS' AND
AC.owner != 'SYSTEM' AND
AC.owner != 'PERFSTAT' AND
AC.owner != 'DMSYS' AND
AC.owner != 'EXFSYS' AND
AC.owner != 'WK_TEST' AND
AC.owner != 'PUBLIC' AND
AC.owner != 'SYSMAN' AND
AC.owner != 'SI_INFORMTN_SCHEMA' AND
AC.owner != 'MDSYS' AND
AC.owner != 'ORDSYS' AND
AC.owner != 'FLOWS_030000' AND
AC.owner != 'FLOWS_FILES' AND
AC.table_type != 'SEQUENCE' AND
AC.table_name != 'RASTER_COLUMNS' AND
AC.table_name != 'RECONCILED_STATES' AND
AC.table_name != 'SDE_UUID_TEMP$' AND
AC.table_name != 'SDO_GEOM_METADATA' AND
AC.table_name NOT LIKE 'F%_SQL_IX1_%' AND
AC.table_name NOT LIKE 'S%_IDX$' AND
AC.table_name NOT LIKE 'S%_PX$' AND
AC.table_name NOT LIKE '%_IX1_%$' AND
AC.table_name NOT LIKE '%_F%$' AND
AC.table_name NOT LIKE '%_H%$' AND
AC.table_name NOT LIKE '%_RT$%' AND
AC.table_name NOT LIKE '%_SDOLAYER' AND
AC.table_name NOT LIKE '%_SDODIM' AND
AC.table_name NOT LIKE '%_SDOGEOM' AND
AC.table_name NOT LIKE '%_SDOINDEX' AND
AC.table_name NOT LIKE '%RT_%$' AND
AC.table_name NOT LIKE '%QT_%$' AND
AC.table_name NOT LIKE '%BIN$%' AND
AC.table_name NOT LIKE 'SDE/_%' ESCAPE '/' AND
AC.table_name NOT LIKE 'DR$XML%' AND
AC.table_name NOT LIKE 'KEYSET_%' AND
AC.owner != 'AURORA$JIS$UTILITY$' AND
AC.owner != 'OSE$HTTP$ADMIN' AND
AC.owner != 'QS' AND
AC.owner != 'QS_CBADM' AND
AC.owner != 'QS_CS' AND
AC.owner != 'QS_ES' AND
AC.owner != 'QS_OS' AND
AC.owner != 'QS_WS' AND
AC.owner != 'WMSYS' AND
AC.owner != 'XDB' AND
AC.owner != 'WKSYS' AND
AC.owner != 'OLAPSYS' AND
AC.owner != 'RMAN' AND
AC.owner != 'ODM' AND
AC.owner != 'ODM_MRT' AND
AC.owner != 'DBSNMP' AND
AC.owner != 'OUTLN' AND
AC.owner != 'CTXSYS' AND
NOT (
AC.OWNER IN (SELECT instance_name FROM SDE.INSTANCES) AND
AC.table_name IN ('COLUMN_REGISTRY','GEOMETRY_COLUMNS','LAYERS','LOCATORS', 'METADATA','GCDRULES','MVTABLES_MODIFIED','SDE_LOGFILES', 'SDE_LOGFILE_DATA','SPATIAL_REFERENCES','STATE_LINEAGES','STATES', 'STATE_ID_GENERATOR','TABLE_REGISTRY','VERSION','VERSIONS', 'DBTUNE','LAYER_LOCKS','OBJECT_LOCKS','PROCESS_INFORMATION', 'SDE_TABLES_MODIFIED','STATE_LOCKS','TABLE_LOCKS','LINEAGES_MODIFIED', 'SERVER_CONFIG','SDE_XML_TAGS','SDE_XML_INDEX_TAGS','SDE_XML_INDEXES', 'SDE_XML_COLUMNS','SDE_LOGFILE_POOL','INSTANCES','ALL_ST_GEOMETRY_COLUMNS_V', 'ST_COORDINATE_SYSTEMS','ST_GEOMETRY_COLUMNS','ST_GEOMETRY_INDEX','ST_SPATIAL_REFERENCES', 'USER_ST_GEOM_INDEX_V','USER_ST_GEOMETRY_COLUMNS_V','ST_UNITS_OF_MEASURE')
)
ORDER BY AC.owner, AC.table_name
