I'm sorry I missed your post.
I implemented Presentation Server 4.0 on Win2K3 at the beginning of last year across 9 terminal servers, 150 concurrent users (running B7333XU7SP22Q1). Everything went well EXCEPT we found that Citrix started becoming very sensitive to Windows Client updates. Let me explain.
Over the past few months, Windows updates become more and more frequent. The client base (more than 500 named users), since the company has used citrix over many years, has various versions of citrix client installed.
What we found was that with the monthly Microsoft patches - various citrix clients would suddenly start having issues. These would vary - for example, from inability to connect to the server farm through to printers not being mapped correctly etc.
Moving to Presentation Server 4.0 and Win2K3 is fine - but be prepared to update your entire clientbase and make sure they are on absolutely the latest citrix client.
I had never seen issues with citrix clients and Microsoft patches before with Metaframe XP and earlier versions of citrix - and it was a pretty nasty surprise when we started seeing issues with the users. Each month (ie, with the latest set of patches) we were seeing groups of complaints with regards to citrix connectivity. I'm sure that eventually, the user community will eventually finally update but it is a gotcha that you have to be aware of.
Lastly, I also encountered some printing issues that required some of the citrix fixpacks. My recommendation is to keep your citrix implementation more up to date. You're going to find that Presentation Server 4.0 is a little more hands-on than prior versions of citrix.
By the way, as far as running JDE on Win2K3 is concerned - the ONLY issue ever encountered is the fact that by default, USERS only have read-only access to directories on the server, and you have to set write access to specific files and directories ! Apart from that, Presentation Server 4.0 works well with every version of OneWorld I've tried !