I just installed ME 2014 (was on 10.7), and I wanted to remove the Derby server from appearing in the list in the Servers window, since I never use it. (Seems like that would apply to a lot of people.)
It used to be removable (in 10.7 & earlier) by updating (un-checking) a plug-in entry in Windows | Preferences | General | Startup and Shutdown, but that apparently disappeared in ME 2013.
I found this old archived posting (from 5/5/2013):
https://www.genuitec.com/forums/topic/how-to-disable-myeclipse-derby/
which gave a “work-around” and said development was looking into the issue. Well, luckily the work-around still works, but it seems like by 10 months and a major release later, it should be easier than this. Like right-click on the Derby server entry and choose “Remove”! Or maybe add a “disable/enable” switch in the Windows | Preferences | MyEclipse | Servers | Integrated Sandbox | Derby entry, like there is for the Tomcat sandbox servers.