A big deal for me was the fact that 1Password ceased to communicate with Safari after upgrading, but the developers were on top of that. A new release is available from the automatic upgrades in the main 1Password application, and new users who download the app won't have any problems with Safari 4. Another mainstay of my browsing world, Greasekit, seems to have come through unscathed, and the InputManager which enables Leech (my current download manager) is working fine for me. Saft also just updated as I'm writing this.
Cover Flow, inside and out
SafariStand was another favorite of mine. It appeared to be working fine at first, but seemingly unrelated issues (like a crash when loading the bookmark organizer) suddenly cleared up when I uninstalled it. I haven't done extensive testing ... I'm working without it for now. One of my favorite aspects of the plugin was the ability to capture thumbnails of history items and, with the included Quick Look plugin, view my website history in Cover Flow. When combined with the bookmark thumbnails generated by WebBla, I had a pretty good-looking interface for searching and navigating my Safari history and bookmarks. Fortunately for me, Apple saw some value in this as well, and this feature is included in the Safari 4 beta.
Safari 4 beta, as noted yesterday, includes the ability to search your history and bookmarks with a Cover Flow interface. The Cover Flow functionality doesn't end inside of Safari, though. Once the thumbnails are generated, they can be seen in any Finder search. Just type "kind:safari" into the search field on a Finder window, set your view mode to Cover Flow (or thumbnails, if you like) and revel in the glory of visual navigation.
Obviously, you can play with the search criteria and narrow the search down using keywords. You can also create a Smart Folder (saved search) for your Safari items and quickly search within it. Users of applications like Ironic Software's Leap will find it handy as well. In fact, Leap handles the biggest drawback, and that's Finder's handling of the filename vs. the title of bookmarks. In Finder, you get the system-generated filename for bookmarks, which looks a lot like this: 00A41A26-F9B3-42FA-90F7-37324C091BF2.webbookmark. In Leap and other search applications, you get the title of the site or bookmark.
I've been generating thumbnails in various ways for a while now, it's hard for me to tell exactly when they're generated (as you visit the site, or as a background process). You might find that your dustier bookmarks require a visit before they'll show up as screenshots.
Update: while this has been working for me, it's becoming less clear that the "thumbnails in Finder" functionality will be readily available to all Safari 4 users. Other TUAW bloggers are reporting that they don't get the thumbnails, so I'm working now to determine which of the various hacks in my system is making it work for me.
Some Mail.app users are having some hiccups as well. Users of the GrowlMail plugin have probably seen some problems, but the fix is easy ... uninstall GrowlMail. You didn't really need the extra distraction, did you? I hear developers are working on the situation now, though, for those who like the extra notification and don't want to use Mail Appetizer (which seems to be working fine, by most reports). There are other reported problems with Mail.app and its interaction with Webkit, the browser engine Safari uses. Check out this post at MacFixit for more info if you're in a bind.