Where you put your code files is really a matter of preference, but I recommend putting them in your home directory. I tend to use "/home/%user%/dev".
IDE: Eclipse or Netbeans. Either is great. Netbeans is closer to emulating a Visual Studio feel, but Eclipse is much more powerful.
I will usually drop Eclipse into it's own directory in my home folder "~/dev/eclipse" because I tend to experiment with different configurations of Eclipse.
I typically use the built in servlet engines but here is a guide for setting Tomcat up independently:
http://developer.apple.com/internet/java/tomcat1.html
The biggest utility I'd recommend learning is either PERL or shell scripting (BASH). This is where OSX's biggest advantage comes to play. Windows still has a shoddy console (everything is backwards!
)
Oh, if you end up needing to use SVN, I highly recommend learning the console commands for it. Every graphical interface for SVN I've found on OSX is awkward or frustrating. I miss TortoiseSVN!