Do not use dots in your links. While it may be perfectly valid, it is not a good idea in general. Some swear by using the full URL/URI (example.com/content/my-content-page.php) over relative URI only (/content/my-content-page.php). I use relative, however, I do see the point in making full references to help with content scraping and may switch somewhere down the line for this reason. Remember, if you use dot notations, something (browser, search engine, whatever) will have to figure this out which may not yield the results you want. It is better to be at least somewhat verbose in your reference to avoid issues down the line.
As far as SEO is concerned, the dots do not add value. While no-one really knows how search engines handle links fully, Google does tell us that they try and resolve all links and URLs so that they are complete. It is not clear if you get semantic credit for links and URLs filled in by Google at all or if semantics is only applied to links where terms are used in the original link. It is clear that the link URL resolver does run as a separate batch process periodically and that by contrast semantics is applied immediately when the link is discovered. It is just not clear if the semantics is updated. For this reason, make the worse assumption you can (to be safe) and assume that the semantic value of your links is based upon the work you do and spell out each link fully.