H.264(!) 1080p MKV's will play better on the EC Player. Everything else (WMV, ASP etc.) on AVPlayerHD.
For example, check out the WMV playback bible at iPhone Life (I can't post a direct link; Google for "Playing Back WMV Videos – the Complete(!) Roundup" and follow the first link). It also states AVPlayerHD is way better than EC Player for that, while also stating the latter should be preferred to play back H.264 1080p MKV's.