A short recipe for upgrading Apex in Oracle XE based on official OTN guide:

1) Download Apex 3.0.1 from OTN and unzip the archive into some directory; let’s assume H:\APEX

2) open command prompt with proper ORACLE_HOME and PATH pointing to Oracle XE instance:

cmd> cd H:\APEX
cmd> sqlplus /nolog
sql> connect / as sysdba
sql> @apexins password SYSAUX SYSAUX TEMP /i/ 

Where positional parameters are:
@apexins | admin_password | apex_tablespace | files_tablespace | temp_tablespace | images

Post installation (assuming we're still in H:\APEX):

sql> @apxldimg.sql H:
sql> @apxxepwd.sql password

(where password is the password of the Application Express internal ADMIN account)