I don't see what the problem is with search when it comes to a well organised file structure - you can either navigate to the folder location manually, or if you know the metadata attached to it (IE if I made a document that contains the phrase 'Draytek 2860' I can search for that) then you can fire up the quick search dialog (Apple+space, WindowsKey on any NT6 platform, I forget the Ubuntu shortcut, think it's just the home key) and enter the phrase you are looking for.
Yes, there are edge cases where you can have multiple similar file names in different folders, but in that case you can get programs that will let you search by extended metadata that they add - IE if you import a PDF from an email attachment, it'll tag it with the time recieved, who it was sent to, from, subject, attachment name etc - Filestar and X1 just to name a couple I've worked with (but not for, natch) which seem to fill this niche nicely. When your document store gets to a certain stage, it starts to make sense to move on to them - or to have a very well organised filesystem that doesn't crap itself after 253 characters of folder/file length. I'm looking at you, NTFS ;-)
For programs, there's metadata too - if I fire up my Ubuntu box in the corner, I can search for photo, and it'll show me my photos directory, and what photo editors I have, the built in webcam booth software, etc on the machine and cursor-key to them if I want. You don't have to search for the specific program name or owt.
I used to be of the opinion that wide search was crap, till I started using it. It also keeps my toolbar/taskbar/launcher clean of the dozens of apps I used to have pinned in them, too. More specifically, it means I can arrange my most commonly used apps in the taskbar, and when the machine boots, I just single click down the list, Super-S, and drag them to the workspace I want them on (one day I'll learn how to have them launch to a preferred workspace....one day) and I can just search for anything else.
And as I've mentioned - many times - before, NewUI/Metro/Whatever search on Server 2012 is actually....pretty handy. Hitting start, Typing group then hitting return is far faster than navigating through the system management console - and as I work on a lot of different servers remotely, it's pretty handy to not have to remember if that particular server has a list as long as my arm of roles and functions that I have to mouse through to find that one function - just hit search, type in the first few letters, hit return.
Horses for courses and all that, but against my own expectations I've come to really rather like it, in general (IE ignoring stuff like the Windows 8 start screen enforcement - I like search, but I don't like the brutality and idiotic way it was shoehorned in) And my filesystem is still nicely arranged into photos, TV, movies and grot, thanks. I might be oh so lazy, but I've still got standards ;-)