iPhone-optimized sites and Web apps are springing up like mad, and so are the iPhone-optimized methods for tracking them. There's mojits, which tries to replicate an application launcher, iPhone Application List, which acts as a software repository with live previews of Web apps (and can be very slow to load on an iPhone), a Mac OS X widget for tracking iPhone apps and others.
While some of these tools have merit -- especially with regard to finding new iPhone Web apps -- we've found that the best way to manage and launch iPhone-optimized sites is with the tried and true Safari (Mac or Windows) bookmarks manager.
Just create a new Bookmarks folder (Select Add Bookmark Folder from the Bookmarks menu), then add any frequently visited iPhone-optimized sites and synchronize your bookmarks to the iPhone using iTunes; in iTunes, select your iPhone from the left-hand bar then click the Info tab, and make sure Sync Safari bookmarks is checked.
This way, if you find a nifty new iPhone Web app while browsing on your Mac or Windows rig, you can bookmark it, making it accessible from the iPhone next time you sync. Even if the page is designed so that it only renders on the iPhone, it will still be bookmarkable in your desktop browser. You won't have to access a third-party Web site to launch your favorite app(s), and the list will be retained, and transfered during the next sync, even if you restore your iPhone, as long as it is still stored on your Mac or Windows system.