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For more intense web-hackery, see the Greasemonkey Scripts and Plugins wiki page.
GraphFi (also on github) is a visualization/navigation tool MetaFilter threads, written by yourcelf. To use this bookmarklet, click the linked bookmarklet when viewing a thread. A bar will appear on the left side of your screen, showing a visualization of connected comments and highly favorited comments. Within the Metafilter page itself, comments that are linked in-thread have a new bracket bit of text: [x replies], and when click on a comment and it will be framed. Click on the [x replies] text, and the replies are displayed below the first comment. This new overlay can be closed by clicking on the close (x) link text on the right top and bottom of the overlay.
See also: related MetaTalk post, where the bookmarklet was debuted.
Bookmarklets for Quoting
Iceberg273 has created three slightly different bookmarklets to help with quoting other people's comments within your own comment. His website, growlers, no longer has his MeFiMarklets [dead link, retained for posterity], but you can find the an Archive.org version of the page. Another MeFite, Jeff Howard, created a different quoting bookmarklet, which MeFite ardgedee then modified a bit.
Bookmarklets for Changing How Links Open
At the randomWalks website, djacobs discusses his two bookmarklets for viewing links found on any webpage. The first bookmarklet alters all the links on the current page so they will open into new windows when you click them. The second alters them to all open in one specific window when you click them. He posted the bookmarklets in a Metafilter thread, just save the links called 'links open windows' and 'links in one window' to your bookmark or favorites folder.
View Deleted Threads/Questions
This bookmarklet opens a new window with links to deleted threads/questions. You should run it from the MetaFilter or AskMetaFilter front pages.
Many more bookmarklets can be found at squarefree.