Quick-ish answer:

Not all of these are effective. More or less, at the moment, the charities GiveWell rates as effective do make it to those lists, but other charities that are clearly less effective also make it to those lists. The lists are not-cause-neutral or cosmopolitan; they tend to include US-operating charities that are likely to be an order of magnitude less effective

In general I would ~not trust their standards much (from an EA perspective) outside of the Charities Working in High-Impact Causes list. But IIRC that list depends on the union of GiveWell, Founders Pledge, and some other EA and EA-adjacent lists, and thus it's arguably pretty good, depending on who is using it and how. Most/all of the charities on that list are plausibly effective (at least someone in EA would probably argue that they are).

In general CN's recommendations include many things we would not see as important for the effectiveness or ultimate outcome, like 'overhead ratio'. See some other posts I made on this (I just added the 'Charity Navigator' tag and a wiki stub fwiw).

Note that there are some EA people in or working with CN, and I see some real promise! Hopefully one of them will chime in here too.

I'll just add that this could be useful to answer because CN is so popular and assumed so reputable, that I've found it hard to convince people to switch from it. So I'd like to still recommend Givewell, but if someone seems stubbornly attached to CN or suspicious of recommendations against it, to be able to switch gears toward a more fruitful and positive conversation about what CN is getting right. So people who use the tool anyway can use it even better.

Looking briefly at their rating methodology guide, I am cautiously impressed with their approach to impact evaluation, considering that they try to perform shallow evaluations at a large scale, at least within-cause. Specifically, it seems to me that they understand the limitations of their models well. 

That said, between-cause comparison doesn't exist, the quality of evidence isn't taken into account as far as I can tell, and there probably are some other issues.

I'll try and take a closer look 🕵️‍♂️

As a side-note,  I was really impressed to see now their donation guide have this article on effective giving  by Dr. Lucious Caviola and Dr. Joshua Greene, which hits all the usual EA points very well. The article itself is the second link on "Giving 101". (It seems to have been written a couple of months ago)