Regarding how we deal with a large numbers of pages which have all been placed in the same folder, the root of the problem is the CMS interface isn't well suited for this, as it has been designed to show the sites hierarchy in full. On our websites we get around this problem by having a number of filters on the data (as apposed to giving the user a massive list) - and it seems a logical solution would be to enable some sort of filtering of pages within the CMS interface as well.
Here are two use cases (and interfaces solutions) to this;
Problem: You're managing your blog, and like us on SilverStripe.com - you've got several hundred entries going back over a year which clutter your screen every time you open the blog folder to add a new blog entry or modify one you've just created (and just realized you made a spelling mistake on).
Solution 1 - filter the folder
In both cases you don't care about the last few years worth of entries, all you care about is the last few entires you made (so you can fix those spelling mistakes), and when you're adding a new entry, you don't want to have to scroll though the whole list to the bottom of the tree - you just want to see a mini list. The solution - give your users the ability to add their own filters (or toggle on and off pre defined ones). In the screen shot shown (2 - Folder with Filter) the filter on the Blog page, means it only shows the last 6 blog entries published.
Solution 2 - dynamic grouping
With each field of any given page type, there are a number of common attributes, such as price on a e-commerce site, or author for a blogs. When you don't know exactly which page you want you need to browse. To help you browse, its useful if you can slip pages into some ("dynamic") groups, which enable you to drill down to find the page you want to edit. In the case of the e-commerce sites, you may wish to group all products into groups based on price, or manufacturer, or for a blog site, you may find it useful to browse by authors (as shown in screen shot.
In the screen shot the blue folders are "dynamic" folders and are not part of the site hierarchy.
I'd be keen on some feedback on this - does it solve the problem of having "lots" of pages within a single category?