hotscripts.com was using GLinks (LinksSQL), however if I am not mistaken, right now they are using custom back-end solution. Regardless of how they are doing it, if you like that type of url structure, you can use Andy's suggestion. But importantly, I would recommend using keyword & category research for your site as that might perhaps enable you to create even more search engine friendly theme structure.
If you follow the instructions I gave you, it would change
First level example: http://www.mysite.com/folder-one/index.shtml
Second level example: http://www.mysite.com/folder-one/folder-two/more2.shtml
It won't affect the detailed pages (unless you update build_detail_url / build_detail_path in Setup > Build Options as well
Also - you would need to setup the 301 redirects from the old category URLs (to tell google they have moved), but thats only if the site is currently live and has been indexed by google etc
LinksSQL is very advanced link indexing system. And yet, there is no option for 'directory' like URLs. Now a days, most CMS, Link indexing scripts, directory scripts - All have these directory type URLs.
You mean for detailed pages? There is no way possible to know what link you are loading, just based on the title... which is why it requires you to include %ID% in the URL somewhere (so it has a way to extract which link its meant to be showing in dynamic mode)
ALL systems will have this problem - its not just a GLinks issue
Are you using dynamic or static pages? (i.e are you running "Build" after changes, or do you not need to run builds for the updates to show up?)
Its not a simple thing to do (the "morexxx.html stuff like scripts/php/software-servers/software/page:2/ could probably be done using some rewrite)
Same for detailed pages - http://www.hotscripts.com/listing/webasyst-framework-136868/ - I think I could get that working as well (again, not the simplest of things to do)
I would need to play around with this on my dev install to see how we can achieve this though. Please email me if you would like me to look into this, and get you a rough price.