Move to junk simply only moves the e-mail to the junk folder. This is use with IMAP e-mail service where automatic filter are applied. Such as Gmail.
Blacklist e-mail blocks exact e-mail address that you have chose.
Blacklist domain means it will block the domain name of the address from the e-mail you chose. Eg. If you have chose to block from a sender jon@spam.com, it would block all mails send by @spam.com from the actual senders e-mail headers.
If you’ve been using eM for a while your blacklist is massive an scrolling through the alphabetized list in a no re-sizable window is a pain. Why not make some better tools? At the very least a re-sizable window to ease the eye strain but perhaps a search function.