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Either one of these three ways will work fine:

1. Download Plugin for Browser
>> For Firefox
>> For Internet Explorer

2. Download Helper Webpage
>> http://aerith.mydns.jp/bin/nicodav/
(browse to the page, paste the video url to the box and click the "送信" button)

3. NNDD2 Niconico Video Downloader & Viewer
>> Ver.0.81 Installer
* This software requires Adobe AIR. Supports both Windows and Mac.

toshichan.selfip.org and vid-dl.net work as well. :D

I prefer getting the videos from Firefox's cache folder:

C:\Document and Settings\<User Profile>\Local Settings\Application Data\Mozilla\Firefox\Profiles\<Random Generated.default>\Cache

And I also sort the folder by Last modified date, so I know which of the random generated numbers+letters correspond to the last movie I viewed

Note:
If you're looking for a video that's listed as sm#####, add .flv to the end of the file
If you're looking for a video that's listed as nm#####, add .swf to the end of the file

To convert .flv to .avi, I used to use Pazera Free FLV to AVI Converter, but now I use AviUtl after watching this video: http://www.nicovideo.jp/watch/sm4614982
However, I don't know any good method to convert .swf's (which are on a compressed flash format) to .avi

None of these alternatives doesn't seem to work anymore D:
Any new ways for 2012, with the nicovideos up-to-date updates?

You can use Jdownloader to download videos from nico nico, here's what i did.

First create account for nico nico, enter the account detail in jdownloader premium tab.

Look for nicovideo.jp in add new account in the premium tab.

Last just copy the video link to jdownloader. The video comes out as .flv

Seems all the plugins and software mentioned above are not working anymore. Right now the only one I can find that still works is houlo video downloader: http://houlo.com/houlo-video-downloader