Now I see why you want to use 3GL from within PL/SQL. Unfortunately PL/SQL is not the best programming language to handle files. UTL_FILE allows you to red/write server side text files (no binary stuff) and that's about it. It will be a lot easier if you can use JSP to write your web application. But I understand we won't have a choice sometimes.
I haven't used Oracle Web/Application Server since version 3.x, so I cannot give you an accurate answer. I thought OAS 4.0 started to offer the capability of hanlding file uploading in the PL/SQL toolkit but I have never used it. You may want to read their product manual. I haven't used the WebDB or Portal product either but I know it is built on top of OAS and uses PL/SQL cartridge or mod_plsql. I remembered seeing a demo more than 2 years ago that one could upload files with WebDB.