The Twitterific iPhone application has a very clever trick: in order to let you interactively add a bookmarklet to Mobile Safari (adding it on your desktop computer then syncing your bookmarks will never be a viable option as long as iTunes will sync all your bookmarks rather than a separate folder specific to your iPhone), it sends you to a page on iconfactory.com that includes the bookmarklet’s Javascript in the URL, and displays instructions to bookmark the page, then edit the bookmark to remove the http part.

It’s a very simple, low-tech workaround that they explain much better than I did here.