First off, yeah virus scanners do point at false positives in hacking tools. This mostly happens with Pokemon ones to me and I am unsure why.
Point 1: Do NOT look through youtube for this question outside of video tutorials for a certain tool (yeah people do this), many use what's first on google which is like... the first big things that were released. Pokecommunity will help a lot but is also sometimes inconsistent on what is the best out there (it's just that some have been at this for years or use a 32-bit system, big project makers don't really tend to switch tools in their toolbox. Can you blame them with how much this stuff changes?)
Point 2: Get a hex editor. I kid you not, a lot of people hacking these games are scared of them. Which is probably one reason why there are 1500 tools.
Alright, here's what I have and it might not be 100%. Yes it's long, I wish it wasn't but that's the nature of things:
-YAPE is still the most stable if you're not doing anything at all to expand stuff or move movesets around. Doesn't have everything they do now but it's just a rock.
-Gen 3 Pokemon Suite is garbo outside of expanding the Pokedex, and that it does well. There are too many bugs from most other functions, location editor maybe works out. Basically the creator had to quit (this happens a lot with tools, another reason why there are 1500 of them). There are some scant things it can do, but you may be better off with using the hex editor.
-Pokemon Game Editor is alright, but last I checked freaks out whenever Fairy Type is around. Also the creator is a bit of a butt but you don't care (just... don't read PGE's advertisement).
-Gen 3 Tools is what I've used. It's compatable with most things, user friendly, has almost every function you could want for this subject, and the other things like item editing are great. Keep in mind though, it autosaves so you might want to backup first just in case.
-PGE or G3T will do about everything here.
-Complete Item Editor is what you want to use to make new stones. It's alright otherwise, but kinda buggy.
-Hex editor for adding effects, see Move Editor.
-I'll be honest, you'll be sitting around a hex editor for the majority of advanced parts of this thing. Adding new effects, etc.. Last I checked people still use MrDollSteak's base for this stuff though.
-For everything else, G3T works best for me.
-Hopeless Trainer Editor is nice and covers about every base. So does Unnamed Trainer Editor. G3T if you don't want to use a separate app. Everything else out there either doesn't do everything (keep in mind, being able to read move list and Pokedex expansion is pretty nice to have) or outright lies to you.
-Stuff like adding EVs and Natures to a trainer is Hex only though.
-I still find the so called Advance Series (sprite editor, sprite position editor, etc.) to be the easiest to use. It even has a rare case of futureproofing in that you can use it with expanded Pokedees.
-I don't usually work with anything else, look this stuff up. A lot I know still use Unlz though.
-GBA pokemon uses Sappy. Most stuff that works for Sappy engines work for that. There are tutorials out there for putting in cries that aren't garbage.
-Advance Map .91 and XSE are still king. Everything else IIRC is still WIP. There is a version of A-Map out there for expanded Pokedexes, you need a hex editor to work with that.
-Use .92 of A-Map if you've expanded the ROM only. This is extremely buggy though and will corrupt anything it touches.
-Also read an XSE tutorial. It's not hard to get into scripting these, but there is a lot to learn.
-Tile editors exist but I don't know much about them. Sorry.
-See mapping. Anything else use a hex editor.
-G3T has Anti-Exploud. It works well but be veeeeeery careful with it. Usually text comes out to different hex than the other data, but it does not descriminate and you should never use it for small things. You can however, make your hex editing troubles much easier with this tool without using it to modify anything: load up your ROM, go to the bottom right text fields, and put in the offending word to find the hex string to search for and how to fix it.
Everything else either has one tool (trade editing), I'm not familiar with, or isn't all that hot (in my opinion). Oh, and I have no clue about megas.