I think we should add http://www.fon.hum.uva.nl/praat/ (Praat) to the list. Seems like this could be used in season 2. (Very mild spoiler below the tag, some might consider it as non-spoiler but better be safe than sorry) Spoiler Seeing how it saw use in tutorials for season 2 and was mentioned in documents for audio analysis edit: And while we're on it, might aswell add the almighty Audacity in case we need to do some audio manipulation
Just my five cents, a website with a ton of different cipher solvers and other tools, many of which are not available on any of the links above: http://www.dcode.fr/tools-list Probably late for the party for what I used it for, but should also be useful in other missions.
whut? that one wasnt on this list? ive used it for any and all vigenere related ciphers. also; it might seem to look like overkill, but this site works better than asciitohex.com --> www.cryptii.com i needed this specifically to translate one of the messages in the NT4 puzzle
Found another interesting tool recently: http://shapecatcher.com/ It's a web app that lets you draw a symbol and looks up unicode characters that are similar to it. The recognition algorithms are far from perfect, but it's still better than just looking up symbols by hand.
OCR is indeed faster and more convenient for large texts in most modern languages, this tool is more to help recognize the origin of hieroglyphs, runes, cuneiform and other special characters.