More often than not I was opening documents, not apps. But with spatial windows in Finder I used to just arrange my Applications folder the way I wanted (sometimes using Aliases) and have it open on the left of my screen, then have my Documents on the right. I kept a row of Desktop icons visible with an In and Out box.

There wasn’t a default folder structure in the early days. Your hard drive had a “System” folder with merely a few hundred files in it (in a hierarchy) that you can ignore day-to-day. Otherwise the whole drive was your playground.