I've done a bit of testing with the J2SE 5.0 timestamp support and jarsigner:

VeriSign's timestamp service implementation does NOT work with
Sun RFC 3161 implementation of timestamp.

The following test service (i.e. TSA cert NOT included in most trusted CA stores)
however DOES appear to work with jarsigner:
  http://www.edelweb.fr/tsa.html

Typical signing and timestamping command (using pkcs#12 cert store):

jarsigner -storetype pkcs12 -keystore mystore.pfx -tsa  "http://www.edelweb.fr/cgi-bin/service-tsp"  mysigTS.jar  <kalias>

Notes:
 (1) JavaPlugin 5 security dialog for signed TS'd Java applet shows extra field verifying timestamp validity.
 (2) A TS'd signed Java applet, targetting  Java 1.4, will appear to be NOT signed if timestamped this way.
       I believe that Sun plans to issue service releases to support timestamped signed JARs.

A sample signed Java applet including timestamping from edelweb TSA is here:
  http://www.jensign.com/JavaScience/www/messagedigestTS/

For testing and comparison, here is the same signed Java applet, but without timestamping:
 http://www.jensign.com/JavaScience/www/messagedigestj2

Note that the signature verification with timestamping appears to FAIL for lower releases of J2SE (e.g. J2SE 1.4)
even though the code was compiled targetting   1.4 version.

- Mitch Gallant
  www.jensign.com