After upgrading to snow leopard, things seemed faster (especially Safari but I don't use it very often.) After I did a full svn update from the code base, compilation was fine but weblogic failed to start complaining about some JMX subsystem issue, then I noticed that the JVM being used by weblogic has changed to Java 1.6.0_b14 64 bits. After digging into the issue, I found out that the /System/Library/Frameworks/JavaVM.framework/1.5.0 changed to a symbolic link which was linked to 1.6. Apparently the snow leopard upgrade made an assumption where we don't need java 5 any more and replaced with java 1.6, to keep the old stuff work, it basically changed all the existing JVM version except 1.3 to symbolic links and point to java 1.6, as well as CurrentJDK. Maybe most java apps still work in java 6 (it should be) and the user won't even notice the switch from 1.5 to 1.6 jvm. However, it's not the case with Weblogic and Flex Builder. To fix the problem, I had to

1. delete the java 1.5.0 symbolic link
2. manually downloaded java 1.5 and move to /System/Library/Frameworks/JavaVM.framework/Versions/1.5.0
3. delete CurrentJDK symbolic link and relink to 1.5.0

After this weblogic started fine but Flex still crashed where the crash report showed that it is still using java 1.6 somehow. I had to manually edit /Applications/Adobe Flex Builder 3/Flex Builder.app/Contents/MacOS/FlexBuilder.ini and added the following two lines to force it use Java 5.

-vm 
/System/Library/Frameworks/JavaVM.framework/Versions/1.5.0

After this change, Flex now can build Flex projects again.

Apple, why can't you let us choose which Java version as default instead of silently removing it.