Long ago when print manuals were the thing, first used pagemaker than later quark express which was quite nice. Haven't used either in years.
Photoshop mostly for illustrations. Someday I need to find a good vector graphics program, for diagram-based illustrations, export to photoshop for final polishing.
Though the output would look horrible by modern standards I was real fond of old mac superpaint which had dual layers, a vector layer and a bitmap layer. Have briefly tried various newer vector graphics programs and cad programs (not recently) but lost patience before getting proficient. The workflow just seemed needlessly slow and arcane though am sure it would get better with practice. Superpaint vector graphics were easy to get what I wanted rather quickly with virtually no learning curve.
The company I worked with the last 20 years before retirement, paper manuals were still fairly important. The business manager of the small company was a great guy, old musician like me. He did most of the grunt work assembling and formatting the manuals. During fall and mid-summer crunch times, he probably did a lot more manual writing than business managing.
I didn't keep up with how he worked but I think a great deal of it was assembled and formatted in ms word. The guy was very good with ms word. I didn't get along with word very well. Word was OK but somehow annoying.
Manuals were collaborative. Each programmer would write explanations of features he had worked on, including illustrations where needed, and tech support and media guys would write what they knew about, then the biz manager would assemble and proof and format the mess, writing additional copy where needed.
We also had a very bright multi-lingual translator. She was heavily involved in writing the manuals in addition to translating the documentation to some languages and hiring out other translations.
The manuals were also exported to pdf of course.
Also involved was context sensitive popup help system. It was so much fun I can't remember much about it. There was some old-style windows help format, that was encoded using ms word. Use arcane formatting commands in word and then run a command line program that turns it into a help file. Then later on, ms decided that mess was a security risk and quit supporting it in the OS so we switched to html help.
Of course, at least at that time none of the windows help docs or formats were easily possible to use on mac, and all the mac help needed editing anyway, different contol key illustrations and different screenshots. I think we went thru two or three different versions of whatever apple thought was the perfect brilliant way to do help files at whatever whim Steve Jobs happened to be in at the time.
The holy grail would have been some format where the manual and the context sensitive help would be the exact same document, so you don't have to maintain two similar but different files for pc, two different files for mac, and then multiply that by however many different languages. I vaguely recall some companies selling rather high price "holy grail" solutions. We never bought into any, dunno if any are good. I'd guess one might need to be a rocket scientist just to figure out how to operate such a tool.
I recall one time studying up on how hard it might be to index context sensitive help calls, pop up help balloons filled with text snipped out of arbitrary places from the main pdf manual. Which didn't seem possible at that time, or at least not feasible without spending lots of programmer hours on it.
Lately for my own use I use open office which doesn't seem much worse than anything else and its free. The couple of freeware programs I released since retirement, wrote html documentation with png graphics made in photoshop. Just looking for clarity rather than "pro formatting". Another advantage is the same set of files can either be included in the downloaded prohram zip for local viewing, or displayed on a web page. No need to convert the same info into two different display formats (for instance html for web and pdf for download).
However that would probably not be slick enough for commercial product targeted at non-geeks.