MyEclipse 3.8.0 GA, released early last week, had a lot of bugs because the MyEclipse team decided to throw in IBM's contribution to Eclipse's Web Tools project which weren't production quality yet. It's the price one has to pay for being too eager.
Thankfully, they made up for their mistake in short order by releasing version 3.8.1 last Sunday which fixes the most apparent bugs. I am sure there are bugs yet to be unearthed, but I used it last night and found no serious problems that prevents me from using it. They even added Sysdeo-style webapp project layout I mentioned before.
For $30 per year, MyEclipse offers a truck load of essential tools for server-side Java developers and unreasonably responsive technical support. Think of MyEclipse as buying timeshare on a talented blacksmith. If you want something done, it's just a matter of screaming the loudest. Highly recommended.