When proofreading, do a 'find all' search for rude words that might not come up on the spell check, that are misspellings of words you would have used (e.g. arse instead of arose, er, misspellings of 'count'
etc).
Save a significant chunk of time for sorting out your references. I've used endnote and zotero in the past, and both have crashed because of the size of the thesis and needed at least 1 day to sort out.
Also the page numbering can take a while to get right, depending on your university's requirements. Some ask for the first few pages to be labelled i, ii etc, and then at the start of the intro, page 1, 2 etc. Make sure you check the thesis guidelines for your department/university. Some are very specific re font sizes, requirements for figure lists, tables of abbreviations.
Don't forget to check your margins are wide enough to accommodate binding. If you are allowed to print on both sides, the margins should alternate between left and right side of the page, apart from the first few pages (all on the left as one-sided). Ring up the printery and bindery (if separate) and ask if you need to make an appointment in advance (mine took a whole morning for the staff there to complete, so I needed a booking). This is important if you'll be handing in around the same time as undergrad courses starting (lots of lecture book printing). Ask them how they want you to bring your thesis. Usually it is in the form of a pdf, so make the pdf early and spend some time checking that it has converted properly. In particular, make sure that each page has the complete number of words (i.e. there's not a line missing off the end of each page) and that any greek/latin/mathematical symbols have converted properly (especially on figures), and that figures have come out looking right and not all squashed.
Make sure you've taken care of the admin side of things - when you hand it in, do you have to take a hand-in form signed by (for eg) your supervisor(s), you department head? If left, this can be a pain if people are away at conferences. Do you need to take ID, proof of fee payment, other things when you hand in? Do you (or your supervisor) need to have nominated examiners in advance?