I think the biggest problem is what you already mentioned: user interface. Trying to cram the features into something that comes readily to hand is tough! That's why I like Clipomatic (sorry... you'd think I got a commission!) it stays out of the way and is unobtrusive. The problem with it is that there is no way to access more features when you want to spend a little more time. As far as the different groups, a tree view might be the best way to go. Since you are using a database, could you make the tree based more on filters? Like the new search features in Longhorn, or the email in Opera M2. You could specify a rule and all clips meeting those rules would go into the nodes that they fit.
One caution, and I don't necessarily think you're there yet, but where is the line between clipboard extender and note software? It's not a clear answer, but as the author you should probably decide. If you go towards more of a note software, you'll get requests for full text editing etc. One thing that I would really like to see is a program that helped you gather clips (HTML, RTF, text, etc) and allowed you to put them into another program easily. That's why I mentioned RTF to HTML conversion. If you could copy HTML, convert to RTF, then paste it into Keynote (another program [and its successor, Keynote 2] I will tirelessly promote!) in three clicks that would be awesome! As such, CHS would not be so much a storer of notes, but an intermediary that would allow you to format your notes and easily place them into the program of your choice. However, any program that allows you to store anything copied to the clipboard will, without a doubt, tread the gray area as a note taking software. Where it goes depends on your vision for it.
Sorry, I may sound retardly serious, as if the fate of the universe rests on this. It doesn't! (thankfully... there is a higher power to take care of this) But, I can see this program getting pulled in all sorts of directions (sort of like FindRun). Just something to think about! Let me say again, CHS is an awesome start... add the Paste 'n Go functionality and I will be happier than... something very happy!