I mostly use eclipse for development (WTP project). Check my post on this blog about my eclipse plugins as well
Before version 3.2 of eclipse I had a simple eclipse plugin for profiling. The link points to a good tutorial for setting this one up for most servers. Problem with this one is that it's not supported anymore and doesn't work with and all above 3.2
Eclipse profiler - plugin for profiling Java applications inside of Eclipse. NOTE! Project is dead and does not work on new versions of Eclipse. Use other open source (such as TPTP) or commercial profilers. SWT components library - set of additional SWT
I tried the eclipse TPTP project. It's a bit overkill but it works. I didn't get it to work using only the project documentation. Note you have to install the AC controller seperately. For the different server configurations I found another tutorial. This one worked for tomcat: eclipse TPTP tomcat howto.
todo: test and describe other server configurations like weblogic, ...