Yes J2EE is widely used.
It is a more advanced version which is giving good competition to .Net technology
But whether J2EE or .Net?
well that is a tough one
It basically depends on which platform you have worked till now.
Since your company is completely upgrading to J2EE then your expertise must lie in Java.
But if you are well versed in Microsoft technologies like VB and all then .Net is the way to go.
J2EE has evident advantages
One it is free
and then all the good things that are in Java are carried to here also and some more.
But not very user friendly. VB.net is very user friendly.
I personally would suggest you go .NET because of all the benefits of using .NET and the windows platform. The windows platform is easier to use and for overall productivity and scince you have the .NET framwork in Server 2003 it is very easy to incorporate. There is a lot of documentation just on MSDN's site for help. Programming in .NET is much more effective because you have up to 26 different languages you can program in and all of them you can interact with. For example if i write a function in C#.NET in a class then you can call or extend that function in VB.NET or C++.NET. Aldo just because something is free does not necessarily mean it is better the reason for this is because usually something that is free, as of now, is harder to use such as J2EE so you might have to pay to get some training, whereas the Microsoft based products are generally easy to use and you can basically figure them out pretty quick.