What are the consequences of deleting any of these?
- How will applications that expect them to be present behave?
- Where will the items on my desktop go?
Those folders are "well known" user folders defined by Freedesktop (check here: http://freedesktop.org/wiki/Software/xdg-user-dirs).
In Ubuntu 10.04 you can edit the file ~/.config/user-dirs.dirs to change the location of those folders. When you've change the file you need to restart nautilus (run 'nautilus -q' in a terminal or log out an in again).
Where will my items on my desktop go?
I am afraid to imagine :-) To be serious - either to your trashcan or straight to hell if you don't use trashcan. I, personally, don't use trashcan, but I have dedicated a separate partition (/dat) to store all my scrap and made all those folders you mention just a symlinks to there (so that /home actually only stores configuration dot-files and so I separate software configs andmy precious data), so, if I delete them, they'll remain in my /dat.
I always delete all except Desktop and Templates without any obvious problems.
If you delete Templates (and don't assign a new user-dir for it), the right-click-Create-Document feature in Nautilus becomes less useful. If you delete Desktop and don't assign it, your home directory becomes the Desktop folder. Which can be a bit cluttered, especially if you have dotfiles shown.