I still still think that displaying the search results in the folders windows will be confusing for new users, and will worsen Pmail's reputation of clogged or clumsy interface.

It should be an option at most. Usually there is no need to see searches in the interface when there is no search. Unwanted info is noise.

I would like the option to display Last Search Results in a specific box. It sort of bugs me that I cannot remove them from my traditional folders box.

I use these folders for mail filters and consider these search results an intrusion. It would be ok if I could chose to move some of them from a Last Searches box into the folders display (maybe). 

Hello!

"Your mileage may vary."
Earlier versions of Pegasus Mail displayed the search results in a way similar to what you have described (i.e. not as a part of the folder listing, but in a separate window). However, the search results were gone as soon as you closed that extra window - to me, that behaviour was not that helpful because I often want to have the search results around for a longer time.

You said you could not remove the search results from your folder listing. Actually, you should be able to do; this is what I am doing all the time (deleting the search results folders if I do not need them anymore), so I am somewhat surprised to read that you cannot. If I select a search result folder and click on the appropriate icon to delete that folder, I get a warning message (à la "do you really want to delete it?"), and after clicking the warning message away, the search result folder gets deleted.

A search result tray can be deleted if it does not contain any search result folders anymore.

What you can do is to enable the automatic deletion of any search result folder. Go to "Tools" | "Options" | "Incoming mail" | "Folder behaviour" that contains a section called "Default behaviour for Link and Search Result Folders". The second option of that section is "Default setting for Search Result folders is 'Delete on exit'" which may do what you want to have. Read the help file to read more information about it.
If you do not want to enable that option, another idea is to set a similar option for a search: when opening a search, you can turn on an option that automatically deletes the respective search result folder. This is similar to the general option described above, but it is valid only to the current search.