After sorting through tons of scripts, I thought I’d share the best ones with you.

Each script is categorized based upon the Javascript library they use. A few links aren’t actually scripts, but rather reference sheets or links to other resource websites.

jQuery (jq)

“jQuery is a lightweight JavaScript library that emphasizes interaction between JavaScript and HTML. It was released January 2006 at BarCamp NYC by John Resig.” – Wikipedia, 01/16/08

Reference Sheet (jq)

Each one of these reference sheets (cheat sheets) are crammed with functions and usage for jQuery. (They are slightly outdated. If you know of any jQuery reference sheets recently updated, please let me know.)
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Reference Sheets (PDF): Page 1 – Page 2

Multiple File Uploads (jq)

The point of this AJAX-enabled script is to give the user a visual sandbox to add/delete uploads, all without ever reloading the page. The examples and documentation are topnotch.
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Fyneworks – Multiple File Upload

Table Sorting (jq)

Sort table data by their parent category with Javascript – no page reloading, compact code, lots-o-fun.
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Polyester – Tablesorter

A List of 240 Plugins (jq)

Rather then regurgitating what’s already on the net, here’s a site that lists over 240 jQuery plugins and their respective links. It’s freaking huge.
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Sastgroup – 240 Plugins For jQuery

MooTools (mt)

“Mootools is a compact, modular, object-oriented JavaScript web application framework, intended to make the process of writing extensible and cross-browser compatible code more efficient.” – Wikipedia, 01/17/08

Reference Sheet (mt)

Being that MooTools is so simple to use, you may not even need a cheat sheet. But just in case, Snook has put together a colorful dab of MooTools knowledge for your enjoyment.
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Snook – Mootools r83 Cheatsheet

mooRainbow (mt)

MooRainbow has to be one the best looking color pickers I’ve seen for the web that isn’t Flash. It’s almost an exact clone of the color picker used in Photoshop, and again, it’s for the web. Sweet stuff people, sweet stuff.
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Woolly Sheep – mooRainbow

Mediabox (mt)

Think of a lightbox, only comprising of streaming online media (like YouTube or Quicktime movies) instead of images. This is what we call a ‘mediabox’, and I love it.
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Ianian7 – Mediabox

Slideshow (mt)

Taken from Electric Prism, “Slideshow is a javascript class to stream and animate the presentation of images on your website.”

The presentation is similar to the default pan/zoom of Apple’s screensaver.
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Electric Prism – Slideshow

Charts (mt)

Easily create stylish charts and graphs of any combination of data, all with Javascript simplicity. If you have any data that needs presenting on your website, this script is well worth a download.
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Copix – Charts & Graphs

Calendar / DatePicker (mt)

Made by the same badasses that created Mediabox (above), this date picker is super-stylish and easy to integrate into your website. Never again should your web user have to manually insert a date.
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Electric Prism – DatePicker

FancyUpload (mt)

FancyUpload is a stylish presentation of uploads and ability to add/remove your upload queue with a mouse click. Well worth a look for anyone presenting upload options on their site.
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Digitarald – FancyUpload

Library (mt)

Keeping with what the header says, this is the motherload of MooTools information – a library for a library, if you will. It’s a complete reservoir of scripts, tutorials, and basic information relating to MooTools.
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CNET – MooTools Library

Mocha UI (mt)

Picture an entire user interface built entirely in Javascript. That’s Mocha UI – expandable, collapse, and minimize windows all while maintaing the feeling of being in a virtual operating system. It’s incredibly smooth, cross-browser compatible, and unbelievably small in size.
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Greg Houston – Mocha

MooTable (mt)

Dress a simple table in a MooTable script and you instantly have the ability to sort any column with the click of the mouse. Easy to setup and extremely lightweight.
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Joomlicious – Mootable

Reflection JS (mt)

Reflection JS beautifully adds a perfect reflection to any image without the need for manual labor. The background opacity, height, and fade can be controlled as shown on the Reflections website.
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Digitalia – Reflection JS

Slimbox (mt)

It’s identical to Lightbox v2.0, only made for MooTools and a mere 7kb in size. It’s a must have for MooTool users needing the lightbox effect.
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Digitalia – Slimbox

MooFlow (mt)

It’s coverflow for the web, built on MooTools. The application is a little shaky, but will no doubt improve with time.
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Outcut – MooFlow

Prototype (p)

“… A JavaScript framework created by Sam Stephenson that provides an Ajax framework and other utilities.” – Wikipedia, 01/23/08

Reference Sheet (p)

Made by the same killer dude that created the MooTools cheat sheet, Snook delivers some Prototype help in the same yummy, cheat sheet fashion.
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Snook – Prototype Cheat Sheet

Script.aculo.us (p)

An obvious must-have for Prototype users. Script.aculo.us provides an amazing library of visual styles (including the ability to drag-and-drop) and works flawlessly on the Prototype library.
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Script.aculo.us

Really Easy Field Validation (p)

Exactly what the header says – convert any form into an instantly-validating machine.
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Tetlaw – Really Easy Field Validation

jsProgressBarHandler (p)

Add a beautiful progress bar to your application and start singing songs of joy. This is by far the easiest (and best looking) progress bar script you’ll find on the internet.
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Bram – jsProgressBarHandler

EditInPlace (p)

This is an excellent script in that it’s simple, yet extremely helpful. The techniques of EditInPlace are used in applications like Basecamp and Facebook, and probably everywhere else on the internet.
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EditInPlace

Prototype Window (p)

Prototype Windows is an extremely advanced version of Lightbox. Create popup windows on-the-fly with ajax calls, or via common href application. Anything’s possible.
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Xilinus – Window/