I’ve been looking for an app like yours for a little while now and am heavily leaning towards EagleFiler for several reasons, not least of which is how responsive you are to requests and questions! It seems like you are working on most of the things I would like to change in the current version, like auto selection of the last library, remembering the zoom level for PDfs etc.
One thing that would be absolutely awesome and would be a key differentiator between your app and the others in the same field like Yojimbo though would be hierarchical tags. This would make organizing my documents etc so much easier and would make searching for them a lot more efficient too I think. Take a look at Keyword Manager for iPhoto. I bought it and absolutely love the way it’s implemented. I think that the website is pretty self-explanatory but if you would like clarifications please let me know. Features like those contained in that app would be killer, specifically hierarchical grouping of tags, auto-completion and the floating windows so that tags can be inspected, added or removed seamlessly.