After the lengthy application, it's tempting to do a terse salary negotiation, call it a day and just start working. Don't throw in the towel quite yet. You don't want to miss out on these great benefits before you sign the dotted line.
Extra PTO days
Most likely an HR person will give you a set number of days during the onboarding process. Most people are content with two weeks per year and accruing more during their tenure, but you don't have to be. HR often has more control over vacation allowance rather than salary.
Work from home/flex schedule
Focus on how working remotely would benefit your productivity (i.e. long commute = less time completing tasks). Understand the organization's WFH policy before the negotiation, and perhaps suggest a trial period of the new schedule.
Sign-on bonus
Common in finance, consulting and IT, this one-time payment in your first check can often originate from a budget separate from your salary. The option is often available during the onboarding process, but many candidates just don't inquire.
Bottom line: if you don't ask, you'll never know (oh, and don't forget to get it all in writing).