I like DS9's packaging best. It's the most simplest. TNG's is okay, though a little extravagant. Voyager and Enterprise's really leave little impression on me. I don't have the packaging, but I don't particularly like it very much either.
TOS has the most overly complicated packaging. I remember seeing something on the Space channel about the TOS boxset saying how much of a bitch it was to get into, and boy did I realize what they were talking about when I got those sets.