Our company is using eclipse since several years now (we are using WTP since release 0.7)
I am currently evaluating eclipse 3.6.2 with WTP 3.2.3 which s
By far the best way for speeding up my projects has been to precompile code that I am not currently using. We have about 20 projects that make up our system and when working on any specific problem I'm only touching a specific subset of those java files. Compiling most of the code that I won't be touching and throwing it into some .jar's, then using that as the source instead of including the projects has proven to speed up things by quite a bit. I imagine it will help you as well if you have 4k+ files. Each project just has a little build.xml that will make a jar out of it to include.
As for the mind numbing slowness in the JSP editing. I have the same problems, it's just so dam slow. I don't have many more than 100 jsp files but I have the same issues as you. My solution has just been to throw money at hardware, which I must admit I enjoy doing :P.