I use Netbeans as my primary IDE because it's easy to work with and has a lot of features. If your doing a web project then NetBeans is probably the way to go as tomcat is bundled in. I have also used Eclipse which is another feature rich IDE and shares several things with Netbeans.
Both of these IDE's throw up a lot of messages as you're writing your code but if you learn what they mean and why they are coming up then it's not a problem, you can know what to ignore. An example is in Eclipse, if you declare a variable that you haven't used then it wil flag it and say something like '<variable> is never used' but you can ignore it as you will use it later. A lot of new programmers get scared by things like this but if you understand them properly it isn't an issue.