The usual suspects: blocks with only invisible attributes (ATTDISP command), annotation scale (command-line version of annotation scale manager -> reset), inherited registered application names (command-line version of PURGE -> REGAPPS), poorly managed extended entity data (depends on the application; ProSteel/ProStructures recognizes a pscheckdwg file[no extension] in the root of C: for auto-purging, AutoPLANT object enabler data requires careful manual removal -> I've banned the object enabler here).