Video to Zune:

To Both WMV AND MP4:
Super Video Converter - Powerful customizable converter for basically ALL media types. Includes Zune preset.

MediaCoder - a universal media transcoder which nicely integrates most popular audio/video codecs and tools into an all-in-one solution

Any Video Converter 2.5.6 - onvert almost all video formats including DivX, XviD, MOV, RM, RMVB, MPEG, VOB, DVD, WMV, and AVI to MPEG-4 movie format for PSP or other portable video device, MP4 player, or Smartphones.

Zilla Free Video Converter-Decompiler - Universal Video File Converter-Decompiler for MPEG, MPEG-1, MPEG-2, AVI (Windows Video), WMV (Windows Media Video), ASF & RM (Real Media).

WM Converter 2 - Extremely easy to use video/audio converter provides file conversion with split and merge options for most popular media formats.

Any Video Converter - allows you to effortlessly convert video files between every format.

Avidemux - Allows for editing videos and re-encoding. Nice if you want to do any touch ups beforehand.

Free Video Converter 1.0 - With Free Video Converter, you can convert your video files into the formats you need.

MediaCell Mobile Video Converter 2.5 - MediaCell Mobile Video Converter Converter introduces unmatchable video compresssion ratio and conversion speed (7 times of the playback).

Free Zune Converter 1 - Very Versitile w/ Batch option. Free Zune Video Converter is a free application which converts the most popular video files (AVI, MPEG, MP4, FLV, or MOV) to Microsoft Zune compatible video format (WMV, MP4).

FormatFactory - Converts between 12 formats including WMV/MP4/DVD!

CinemaForge - This combination video-conversion and creation tool boasts good speed and a nice set of features. CinemaForge's polished interface is both handsome and rather simple to understand.

To Just WMV:
Encode360 - The converter for MS products (XBOX360/Zune). Includes Zune preset

Windows Media Encoder - A powerful tool for converting both live and pre-recorded audio and video to Windows Media Format.

M2PMCEncoderZX - Specifically built for the Zen, but works fantastically for the Zune.

ZuneTvWatcher - Convert Recorded Media from Media Center PC's and other video to Zune

To Just MP4:
Twins Video to iPod-Zune-PSP-3GP - Convert your videos and take them with you on your portable devices (WMV doesn’t work)

PSP Video 9 - It can convert regular PC video files (avi, mpeg, etc) into PSP (and Zune) video files.