After much searching, I've found a suitable (& free) replacement for VectorNTI, A Plasmid Editor by a guy at the University of Utah. It reads GenBank files, so you can easily import your VectorNTI files. It works on both Windows and Macs, and unlike VectorNTI, it doesn't hide away your files in a database, so you can easily work on stuff both at home and in lab. Further, it reads ABI trace files (which I don't believe VectorNTI does), performs alignments, and even speaks text out-loud, which can be really useful if you're, say, comparing your sequence to something printed out. It only took a few minutes of poking around to become familiar with its intuitive interface. This was clearly designed by someone who has actually cloned stuff before: an excellent program.
PS Just discovered that you can make a reverse complement of an ABI trace file (and immediately align it) -- very useful if you sequenced something with a reverse primer.