One click, or you can set it to run automatically on shut down, etc. Saves time from doing it manually and is more thorough.

Your second question about pop ups, I don't know.

For blocking pop-ups, I like the Google Bar. It works great, and it's free. Look here:

http://toolbar.google.com/

For reviews of various Internet washing software, try this link. I think you'll find all the major products reviewed there:

http://www.privacy-software-review.com/window-washer-review.html

Try Mozilla, I haven't seen a popup in ages.  Also has great control over cookies.  You can use Firebird, which is Mozilla but just the browser (no email, chat, address book, etc.).