Get a passport wallet that can store your frequent flyer (or hotel) membership cards. That way you always have them when you travel.
There are also a few apps for that if (like me) you tend to have 90,000 different cards and don't need to present them for lounge access or whatever (I am status-less).
I do like having a passport cover, though, because it can be handy to tuck things in the sides.
1. Mark your visa with a Post-It flag, so that it's easier to find the right page, and the border agent doesn't spend ages looking for it. You can just open right to it.
2. If you're running low on pages, reserve a few of the last blank ones by sticking a regular Post-It on the page. Then you don't have to worry about lazy immigration officials wasting one of your last visa pages for a single stamp.