There are pro's and con's for both. The type of hosting you have also influences the answer.
Assuming shared hosting, Mostly use of different users on the server for each domain is the best practice. Added security is the primary benefit, however there's also an advantage with procwatch (dreamhosts daemon that acts as a gatekeeper on shared hosting preventing resource hogs).
Where you may want to use the SAME user is for staging sites. For example you're running example.com and also have a sub-domain called stage.example.com that's not open to the public (require basic authentication using goodies -> htaccess to achieve) where you are working on the next version of the site. It's much easier to move that site to the main site if the development site is using the same user.
Edit to add:
A more specific reason that a user per domain, rather than one user for all domains. Example: Your WordPress install get's hacked because of flaw in the theme on site A, If sites B, C, D, E, F are all using the same user, then they have all been compromised. If B,C,D,E,F are all running from unique users, then most likely only site A is compromised.