Although there aren't 'good' and 'bad' endings per se (they're all a version of 'bad'), I think you're certainly supposed to feel that the 'riding off with Panam into the sunset' ending is the best of a lot of bad options. For me that was the worst one though; it's quite generic and just... bleh.
The Arasaka ending is I think the one you're supposed to view as the 'worst'. But the Arasaka ending for me was the best; it's haunting, clinical, twisted, and very unique. I'm glad I picked it the first time around.
Relinquishing control to Johnny is a pretty cool and unique ending too. It plays on one of the stronger aspects of the main storyline (the times you play out the body swapping) and it shows just how much V changed Johnny's character, not just how Johnny changed/started to takeover V. It's up there with the Arasaka ending.
The 'choosing the easy way out' ending (i.e. committing suicide) is quite good too, oddly enough. Abrupt, obviously, which is the main downside to it, but the reactions from some of your friends to your death in the credits are excellent, especially Judy's.