This is a tricky item for me too; I use the stock email client on my Note II.
My pop3 Note II inbox can delete from phone w/o affecting the server inbox.
I have folders on the server in my imap account so that, when I delete an email on my Note II, that email in my customized folders isn't deleted. (I just have to remember to move the emails to the folders.)
When I delete hotmail on my Note II, it also is deleted from the server; however as long as it's in my Note II "trash" it's also in my server hotmail "deleted" and therefore still available (and can be manually moved back to the inbox). Hotmail is considered (by my Note II) to be exchange.