I often give a z-index of 9999 to elements that need to always be on top but in the end I often find exceptions where another element also needs to be on top (at certain times) that I hadn't accounted for so I end up sticking another 9 on the end so I'm probably no better off than if I had used a lower number to start with. It's one of those things that you can't always account for an no matter what you try there will always be exceptions where you need to adjust the stacking levels.
However in a complicated stacking environment I would avoid using z-index:1, z-index:2, z-index:3,4 ,5... and so on because at some stage you may want to insert an element between two others and you wouldn't be able to do that unless you then revise all the other x-indexes above it. Much better to start with z-index:1,z-index:10,z-index:20; z-index:30 etc. That will leave you plenty of options to insert any elements between.
In normal layouts though it shouldn't really matter as there would normally be few stacking levels to worry about.