Some important information to read:
1. About WMV
Windows Media Video 9 (especially the later SMPTE-compliant VC-1 implementations) is comparable to H.264 Main and High Profile. While WMV9/VC-1 does have certain advantages over H.264 such as support for non-square integer transforms, H.264 is more consistently able to yield better picture quality because it supports multiple reference frames, reference B-frames, context-adaptive binary arithmetic coding (CABAC) and stronger in-loop filtering. H.264's quality advantage is typically more evident at low bitrates.
2. About H.264/MPEG-4 AVC
H.264/MPEG-4 Part 10 or AVC (Advanced Video Coding) is a standard for video compression, and is currently one of the most commonly used formats for the recording, compression, and distribution of high definition video. The final drafting work on the first version of the standard was completed in May 2003.
As you can see, overall H.264 is a better choice than WMV9 for the time being.
However, you can run a test yourself by converting a video to both H.264 and WMV9, and if you don’t plan to invest any money on it, I recommend you use MediaCoder or Quick Media Converter.