Recently I read a blog post Use WordPress as an Evernote replacement and quickly caught the idea that it could finally solve my main problem as I try to store too much loosely related information and wiki based solution didn't meet my expectations in this particular case. I need to note that I only consider self hosted solution as I do not want to depend on third-party services.
Personal scrapbook needs to store notes/ideas/bookmarks/files and organize entries by using tags/categories, provide search functionality and easy way to restrict access to the whole website.
The most important plugin is the Restricted Site Access as it provides easy way to lock down entire website. The rest is up to you. All I can suggest is to check out plugins: WP jQuery Lightbox, WP-Syntax, WP Hide Admin Bar, Login Security Solution and WP-PageNavi.
Do not forget to use Press This bookmarklet.
First solution is based on P2 theme by Automattic.
It provides pretty nice user interface optimized for short notes which is very usable on tablets as you don't need to leave main page to add new entry.
Second solution is based on Themolio theme as suggested in the earlier mentioned blog post.
It is not optimized for tablets so it would require couple of small changes but the grid layout is an interesting idea.
This theme doesn't offer easy way to add new entry on tablet so I suggest to use Wordpress application.
I decided to use Themolio theme and modify it a bit. After playing with it for a couple of days I can say that finally I am happy with this solution as I can quickly add and organize new information and search it later. It is quite ironical that I am using WordPress here for couple of years and tried so many different solutions to store personal scraps but not the WordPress itself.