Okay, step aside...
1) Botania has information on nearly every item it adds, with everything available from the beginning so that if you see something you want to craft, you can find out what it does without having to grind through lower-tier items just for an explanation. The only restriction on crafting anything is by how much mana you have and the amount of items you have available.
2) Thaumcraft. At the start, you have very few items available for crafting, and the progression is through a ton of research. Plus, the more powerful items are usually made with a bunch of resources anyway, so that means that in addition to stockpiling and crafting a lot of stuff, you have to do any research necessary first.
3) Witchery. Yes, there are some books, for basically each stage of your "tiered" progression, but not for a lot of the other stuff that you need/want in between. Hence the wiki. But, I don't think that's the best solution available for some, especially those (like me) who don't have a constant internet connection, or enough computer power to run a browser and minecraft at the same time.
4) HQM. First of all, the amount of information that you can put in it is virtually unlimited, but the nature of the mod means that it is written for a specific world with a scenario, right? Thus, not available for use outside of that one world. Unless it's possible to include documentation on mods out-of-the-box, it's not a very feasible way to be a "manual" of sorts.
I think that all the information on a mod should be made available offline in some way, either as a downloadable document or as an in-game book, or a whatever. This doesn't mean the death of wikis; all I'm saying is that the information should be made available to as many people in as many ways as possible. Wikis have the capability to post videos and maybe add a place for discussion, but for a clear, concise explanation, there should just be one file that has everything, I think.
Back to Thaumcraft; I do like the visual representation of progression. You know, the "track" of the paths through the thaumonomicon? Botania doesn't have this feature, quite as much, at least. My suggestion: something like "suggested reading" after an entry in an in-game book, that has a list of other entries that expand on or use said entry.