These are the ones I’ve got installed, and I find them all very helpful:
Ultimate Timeline - Immensely helpful for scheduling lessons and reviews. If I could only have one script installed, it would be this one.
Dashboard Progress Plus - Great for knowing how close you are to Guru for current-level items.
Niai Visually Similar Kanji - It’s easy to get similar kanji mixed up. When I get a mix-up, this script lets me compare the differences right away, and I can also see what else is similar when I’m learning new ones.
Keisei Semantic-Phonetic Composition - I have this for “The More You Know” 
but it’s actually pretty helpful for knowing how close some of the radicals are to Kanji meanings. Sometimes I’ll add synonyms to radicals if they don’t already match the Kanji meaning, based on this script.
Dashboard Leech Tables - This is a nice way to keep track of items that might be giving you some trouble. I have the Leech Threshold set to 2, as that way it shows actual problem items instead of stuff I just typo’d.
Hide Context Sentence Translation - I like to try to translate the vocab example sentences first before reading the English. When the English is right there underneath, it’s hard not to see it even if you’re trying not to peek. This is a handy-dandy little script that lets you translate in peace and then see if you were right.
For third-party sites, I always use these two:
KaniWani - Reverse recall for the vocab is extremely helpful and important. KaniWani really helps me nail the order and reading of vocab words, and I know both the vocab and the Kanji so much better once I’ve done them on KaniWani. Definitely make use of the “add synonym” function in the later levels as actual synonyms start to pile up.
WKStats - A wonderful stats site that shows you where you’ve gone, where you’re going, and how you’re doing overall. Great to play with the projections and see if you can challenge yourself to meet your speed goals, as well as see how your Kanji knowledge stacks up alongside Japanese grade-school lists and JLPT lists.