The New Equipment Manager is nice, but it's also pretty basic. You choose to save a set, choose a name and icon for the set, and there you go. You can drag the new icon onto your toolbar for quick changes, at least, but there's not much else. You can't synchronize it with a talent change. You can't set events to automatically change sets. Because of this, or even because of straight up familiarity and the issue of remaking all your sets in the new system, I'm sure a lot of people will stick to addons like ClosetGnome and Itemrack (if it ever updates).
Equipment Manager certainly isn't the only example of this. I still use Parrot over Blizzard's default Scrolling Combat Text because I like the ability to segregate information and adjust the scroll fields. I don't think I've heard of one guild abandoning their Ventrilo server for Blizzard's in-game voice chat. The in-game threat meter still doesn't hold a candle to Omen -- not that it's as crucial to monitor threat these days, especially in the pre-raid game.
Still, there are advantages to using the in-game systems as well. It's nice to know, for example, that on patch day, as long as the game is stable, you'll be able to boot up, log in, and get that functionality immediately instead of hoping the addon author has managed to get their addon compatible to with the newest game version.
So anyway, I'm wondering. For those of you who have used addons for scrolling combat text, equipment management, and the like, have you switched over to Blizzard's versions, or are you plugging along with your existing addons? Why?