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I'd like to create a GUI that displays a tree, some text boxes, buttons, and then as a panel, a fully-functional notebook. Is that possible?

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Try putting a PaletteNotebook where you want it. – ssch Jan 9 at 21:15
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Are you sure you want to use GUI-kit? Since the arrival of version 6, more than 5 years ago, this has been been pretty much been obsolete. – Sjoerd C. de Vries Jan 9 at 21:43
Well, no, actually. I want to embed it in a GUI constructed in java. I thought I came across a way to do this in the documentation, but I can't find it now. @ssch, thanks I will check that out. – Max Jan 10 at 4:36
Maybe with "native Swing": djproject.sourceforge.net/ns/index.html But why do you really want to do that and not use CDF right away? – Rolf Mertig Jan 10 at 16:41
related: mathematica.stackexchange.com/questions/5603/… . the "solution" there is to host an HTML page that contains the CDF object in an HTML View, which I'm sure the Java libraries have. – amr Jan 10 at 19:44
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I realized just now that I never came back and explained how I solved this problem. I used the MathSessionPane class provided in JLink:

http://reference.wolfram.com/mathematica/JLink/tutorial/WritingJavaProgramsThatUseMathematica.html#11599

It's not a fully fledged front end like you'd see in Mathematica, but it worked quite nicely.

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