Firstly, what would one recommend as the best window size for a project, if I want it to be able to be used by many, embedded on websites, and be a relatively large size.
The default 640x480 is a good size for a display that fits on most screen sizes while not being too small.
econdly, I read the blog post on the audio formats. Does this mean that, for the foreseeable future, I have no options for audio that is supported by all browser types? If that is the bleak case, what format would I be best off choosing?
Maybe you missed the point of the post. Construct 2 converts all your audio to Vorbis (.ogg) and AAC (.m4a) for you, to get around this issue. (You need Windows 7 to encode .m4a though.) So you need two formats to cover all browsers, but Construct 2 helps you do this.