I am looking for an HD camera (at least 720p) that has an audio input for a microphone and I can use for simple shoots. No need for much in the way of manual controls. Manual focusing would be nice. Price would be under $1,000. Any suggestions?
A huge range of choices Sean. To adequately choose, you should do a lot of research. The Canon T2i or T3i is great, since this is a Canon forum, we are a bit biased. But I also have seen great stuff shot with a GH2. Sony's new little cameras are also getting rave reviews.
Understand your goal and things will be easier. For example, if you need true camcorder ability (clean zoom and long running times) then a Panasonic or Canon camcorder is the better deal.
If you want to have interchangeable lenses, great depth of field, then go for the HDSLRs.