The URL structure of your site is something you should be putting some thought into. It shouldn't necessarily be a reflection of the way your site is physically laid out (i.e. which parts of it are hosted on what machine) but rather a reflection of the way you view the relationship between the different parts of your site and, from an SEO perspective, the way you want the search engines to view this relationship.
There may be times when you want to separate out different sections of your site (such as a news section or a shop section) you feel should remain under your site's domain name rather than split off into a different domain. But should you choose a sub-domain or a sub-folder structure?
For branding or simple convenience purposes, it might make more sense to split off a few sub-sections and give them their own sub-domains rather than sub-folders. You may also want to avoid overly long URLs and feel that sub-domains are a good way of achieving manageable URL lengths. But what are the SEO implications of sub-domaining? You may think that sub-domains and sub-folders would be interchangeable as far as search engines are concerned but in reality they are viewed differently.
Sub-folders (i.e. www.domain.com/subfolder) are easily recognised by the search engines as part of the same domain and therefore are seen as part of the same overall website. Sub-domains (i.e. subdomain.domain.com) pose more of a problem to the search engines because they can either be a part of the main site (blog.company.com) or owned by different companies altogether (as is the case on blogging networks, shared web hosting, etc.). The fact of the matter is that search engines find it very difficult to tell the difference between related sub-domains and unrelated sub-domains and they generally err on the side of caution, treating the sub-domains as separate entities, which can be both good and bad from an SEO perspective.
On the one hand, inlinks to a sub-domain are likely not to build up authority for your main site and vice versa. This can be problematic if, for example, you are trying to use your content-rich company blog as linkbait but are hosting it on a subdomain. You may well end up with a very high ranking blog but a pretty low ranking main site. Unless your blog is really a standalone entity that can be monetised separately from your main site, then you may have just wasted a lot of time and money generating optimised content for nothing.
On the other hand, many search marketers use sub-domains as means of getting more results into the search engines, getting around Google's 2 pages per domain limit and pushing their competitors out of the way. Although the official line from Google is that this has now changed, the reality of the search landscape is not entirely convinced, for the time being at least.
Unless you are planning on using the above competitive (but ultimately short-lived) SEO tactic, your main concern should be balancing having clear distinctions between the different parts of your site and making sure all different parts get the appropriate amount of authority and link juice.
Ask yourself, how much of a separate entity do you want a particular sub-section to be?
As sub-domains, different parts of your site would need to be treated as separate websites as far as optimisation is concerned. The upside is that interlinking them could mean more link juice is passed around different parts of your site, although this may change as Google and Co. find a way to recognise related sub-domains as parts of the same website and treating the links as internal.
Using sub-folders, you would be concentrating your efforts on optimising one site and not spreading yourself too thinly. Most SEOs tend to recommend using sub-folders as a default URL structure exactly for that reason, unless there is real need (branding-related or otherwise) for using a sub-domain.