Currently I have both IDE's installed, both do the job of compiling my in TeX written TMAs to .pdf documents. The TMA sets I sent in were close to 20 pages and contained several TeX and external images.
I haven't decided yet, here are some preliminary thoughts.
TeXnicCenter is modelled after Visual Studio ( I suppose ) while Texclipse is a plugin for the Eclipse platform.
Both applications are free.
No major new functionalities seem to be planned for Texclipse. The last bugfix-only release was in mid 2008. It looks as though Texclipse will be abondoned soon. The platform Eclipse is updated regularly.
For TeXnicCenter work on release 2.0 has been started.
TeXnicCenter is closed source, while Texclipse is open source Java.
Sofar about comparing the two. More on functionality after I have completed my next TMA. I´ll prepare the TMA with Texclipse.
More later.