It sounds like you need a database to store your Vectors' data. Whether you store it in flat files as serialized objects, or you put the relevant data into a database, you need to have some sort of naming/identification scheme to figure out what is where. You could write each object to its own file, and keep a list in memory that lists what Vector is stored in what file-- a HashMap is good for this - the key is the "Name" of your Vector and the value is the path (File.getCanonicalPath()) of the output file.
Other general suggestions: use an ArrayList instead of a Vector, if possible, since it will take less memory. Are you using the
java parameters -Xms1024m -Xmx1024m to increase the size of your Java Virtual Machine (use a smaller number if you do not have 1MB of RAM).
Hope this helps,
Joseph