Curently we have ArcSDE 9.3/Oracle10, and layers in SDEBINARY.
It is possible to make queries with SDE.ST_GEOMETRY or SDO_GEOMETRY commands ?
With ST_GEOMETRY and SDO_GEOMETRY you can use SQL in addition to ArcGIS Desktop to work with your data. Although with SQL, one should take many precautions (read the docs).
To migrate from sde_binary to one of above, you have to reload all data into your database.