Stuff like vdig, copystock, jobs, and workflow basically just automate a lot of the micromanagement, so I don't consider it a big cheat. Vdig is the tool I used first and I use it the most because digging out veins by hand takes forever. Haven't used jobs and workflow too much yet so probably not using them to potential, but being able to make stuff out of specific rocks is good, and I like having workflow auto-suspend cancelled jobs. Copystock is great if you're using a lot of custom stockpiles.
Fixwagons/merchants/diplomats are just bug fixes so I don't consider them a cheat. The water level toggle is a useful feature too, if I'm filling up a water/magma tank, seeing the numbers is useful, but this lets me turn it off when I don't need it without saving and reloading. The idler display can be turned on and off too, but I usually just leave that on. Fpause is okay if the game suddenly freezes on me, and I admit I use the die command to savescum easier.
There's also the Stonesense launcher which I count as a seperate feature.
Reveal and prospect are kind of cheaty, so I use them sparingly. I like that prospect can be used on the embark screen now, it saves the trouble of embarking on a spot and finding nothing but junk. You can also prospect multiple biomes on an embark too, which helps to maximize the amount of useful ore you can get. I only use reveal to see where the soil layers are on the surface, and to spot surface aquifers. I do this to plot out my farming areas first to keep the fortress layout more efficient. It's also helpful to see where aquifers that are above your fort entrance are if you embark on some hills, because digging into them from below seems like a good way to screw the fort. I don't check out the caverns with it, that's what exploratory digging is for. I have looked at the caverns on experimental embarks and stuff though, but not for main forts.
Most of the other stuff is basically cheats so I usually don't bother. I don't use the cheats to fix mistake I made, but mostly to fix problems in the game that are the result of bugs or something.