Hi, I am finishing my PhD in astrophysics and also working as a software engineer. I also co founded a company (yes I am a technical cofounder as well). I have similar thoughts about scientific publishing. Even journals where highly values places you can publish has significant impact on your carrier. Often I use http://arxiv.org/ and but the functionalities are very limited. I also use http://www.mendeley.com/ to manage my papers. I honestly believe somebody need to do some work on this space to make this process more efficient and unify many fields who has their own places to post papers. Let me know what you think, I am interested in talking to you further about this idea. you can email me at peiris.prabath at gmail.com