Main thing I miss is the lesser degree of abstraction in doing anything. If you wanted to build a simple app which just took one input and did a calculation and returned a result, there were multiple languages, but you didn't need a huge number of libraries, infrastructure, etc. to deploy it -- you just built the code, compiled it, and distributed a binary (and source, with a makefile). There was complexity crossplatform (even across unixes), but there was a period of time in the mid-90s/early 00s where "some form of linux or a BSD" was all I had to care about, and it was pretty easy.

Also, being able to trivially modify almost anything I used (because it was largely open source, and simple).

Lots of things were worse, but less abstraction was pretty nice.