Keep in mind a couple of differences between 3.0 and 4.0 releases in terms of connectivity and using a previously installed Oracle client....
1. They both come with different default versions of the JDBC driver, and 4.0 requires at least an 220.127.116.11 version of the driver
2. Release 3.0 automatically tries to find both a tnsnames.ora and a JDBC driver in an existing Oracle client install (often doing less than a perfect job).
3. Release 4.0 instead gives you control of which Oracle Home / Instant Client to use. See options in Tools > Preferences > Database > Advanced
4. Both 3.0 and 4.0 also let you specify in Advanced which directory to use to look up a tnsnames.ora, which need not be in an Oracle Home.
Since you can still connect using SQL*Plus or SQL Developer 3.0, this does not seem to be a firewall issue (e.g., something changed over the weekend).
I would recommended verifying the connection details in the 3.0 and 4.0 user settings are the same, plus check the preference values set for points (3) and (4) above. Is it possible you have more than one tnsnames.ora* file, and 4.0 is somehow picking up a different copy than 3.0, one with incorrect connection info?
SQL Developer Team