Thanks for the insight guys, as I wasn't too sure if there was any reason for choosing one over another. My current host allows for 3 or 4 subdomains, which can be created easily in the control-panel, but long-term, what if that isn't enough? At least folders can be added without limit.
I was originally thinking that if it didn't matter either way, in terms of administrating the domain, or affecting its efficiency, which web-address format sounded easier to remember. One of the things I have been wanting to do for a while, and now have the chance to, is split off the main non-TFs toy sections (Lego and GIJoe to start with), and house them (and TFs) under a main toy-fan umbrella/mainpage. In the end though, I figure that if people can remember the main domain name anyway, it will be indexed to guide them to the desired themed subdomain or folder - and as such, if folders are easier to work with (I'm guessing, less clutter of files in the main domain folder?), it is probably the best way to approach this.

As for the cookie issue - I'll have a look into it as I never realised it was a problem. I figured 'www' was part of the address, so never thought that browsers would bring up anything from my domain (I thought the www would need to be manditory to access sites that have it in the address). I just tried it, and the main domain comes up with forum articles that are over a month old, which would probably be that cookie issue you mentioned.