Stimulating post, Durbrow. A haxie enthusiast myself, I read Tog's article with keen interest. As to your questions:
Don't know if it is Application Enhancer or Menu Extra Enabler that is at fault, but I can't get the latest versions of WeatherPop or WeathermanX to launch from the menubar, could be the apps themselves not up to Panther. (Out dated WMX still works fine, though.) Other than that, since doing a fresh install of AE and all my haxies in Panther, everything seems to be working flawlessly. And dang, have I got haxies...
As to Panther's UI shortcomings, as particularly addressed in The Good, the Bad & the Ugly, some of Togs points may be just a wee bit overblown. Yeah, I hate label colors in Panther too and check obsessively at the Unsanity site for an update to Labels X, which looked spectacular in Jaguar. But I don't get all his objections to the Finder, which I find absolutely brilliant, and frankly I resent being told how to customize my own Mac.
FruitMenu is the greatest thing since sliced bread, glad Tog likes it nearly as much as I do. And Contextual Menus are fully addressed in FruitMenu's Preference Pane under Help. I love being able to move items between volumes instantly; FM makes this and other neat tricks possible. And as in Classic, FruitMenu allows you to put your entire HD into the Apple Menu in any configuration and navigate through it rapid fire with but a single click. Plus it allows you to assign hot keys. For only ten smackers, FruitMenu has got to be the best value of all Unsanity's offerings.
(AliasMenu is another convenient little hack that allows you to place multiple menus with customized icons in the Menu bar. Unfortunately it can run rather slowly when called upon to display large icons/submenus. But it does make efficient use of otherwise wasted real estate in the Menu bar. Still overpriced at what, $25? But I digress...)
Couple other little complaints of his, about Safari Import/Export and Application Switching: hidden features can be activated with Safari Enhancer (free!) and you can see and switch running apps with Command Tab.
Still, Apple should enhance Safari by default, and I don't understand why we still need third party apps just to bring back the functionality of OS 9. I payed more for haxies than I did for Panther!
Sorry for running on; had I the time, I'd been briefer...