I use several tools with ED. Over the time I have switched between what I use, but here is currently what I run.
Voice Attack with a heavily modified KICS profile. I have it at the point that I can use it with or without the mic. So when I don't feel like using a headset I can still get the benefits.
ED Tracker. This one is new, less than a month old. But My god what a difference to this and other games such as War Thunder and CLOD.
ED Market Connector. I may not be trading, but this tool helps me contribute back to the community. It takes the Commodity Markets, Shipyard Data, Outfitting Data, and Station info and sends it all to EDDN. It gets activated every time I land at a station or outpost.
Trade Dangerous is my goto for trade route planning and for checking when I need to actually find some commodities. It also is where I can do a quick lookup of shipyard data.
Inara is my goto for keeping track of what I am flying and my ranks, achievements, Credits, and other information that can't be tracked anywhere else.
Captains Log is what I used in the past when exploring, and when I finally decide to make another trip out of the bubble, all my finds will be kept track of in this gem of a program.
When I am looking for things such as stations or commodities and the numbers don't add up, I use Thrudds and EDDB.IO to double check things.
For configuring ships, its Coriolis.io and that is it. I used to use ED Shipyard which is great, but Coriolis is cleaner and has more valuable information at a glance.
And lastly, when I am looking for new tools, or something else ED related, I use ED Codex. The best list of ED Things out there. Easier than searching forums, and if it is not in the ED Codex, then its google foo time. If all else fails, I ask on the reddit ED Sub.