HI,
Well personally, I don't know anything about teh NTFS change journal, but from the other two options I'd pick the Archive bit method rather than modified time, purely because I don't like relying on nothing screwy happening to the system date and time on the server.
In reliability terms I can't think of any reason for concern about the reliability of differential backups. Given the choice I'd prefer to only use Full backups, but I'd rather have differential backups than incremental backups any day. Not just because it takes less time to restore the data is required, but also because you're not as reliant on a series of tapes not having problems, and if the worst does happen, and your most recent tape becomes faulty, you can still just move back to the previous one.
One thing to note however, if memory serves correctly, SQL data is always backed up as a Full backup, as Backup Exec can't delve into the database and pick out only the data which has changed, so you won't see any space saving from backing up that data using a differential backup.