Install VLC Media Player (opensource/free) which can be downloaded from http://www.videolan.org/vlc and supports .MOV format, then open your video file by going to Media > Open File… and browsing for your file or, by just dragging and dropping your video onto the VLC player, then choose Tools from the Menu bar and select Effects and Filters and on the Video Effects tab, tick the Transform check box and choose your degrees of rotation. The video is rotated counter-clockwise, so to rotate clockwise 90 degrees you’ll want to choose rotate by 270 degrees. -Tech Talker
If recorded in landscape, the video should work fine in WMP. My understanding is the iphone sets rotation flags in the video stream which Quick Time can read and make the adjustment. WMP cannot or doesn't seem to use these flags.
A fix for your sideways movies is this:
1. Import the video clip into Windows Movie Maker.
2. Drag the imported video clip and drop it onto the timeline.
3. On the Tools menu, click Video Effects.
4. To rotate the video clip to the right, drag the Rotate 90 video effect and drop it onto the movie on the timeline.
To rotate the video clip to the left, drag the Rotate 270 video effect and drop it onto the movie on the timeline.
5. On the File menu, click Save Movie File and follow the instructions in the Save Movie Wizard