For better SEO, I would use WordPress as the overall site (not a subdirectory or a subdomain) and continue to upload your sample applications as separate PHP pages and link to them from within WordPress.
WordPress with a good SEO plugin will automatically generate your sitemap for Google as well as handle multiple paths to the same content (via categories, tags and/or other custom taxonomies) and apply rel="canonical". Overall, it more or less forces users into decent SEO practices that, if left to their own devices, they otherwise would not do. If that previous sentence describes you, there you go.
On the other hand, if you are an inveterate hyper-tweaker and can think of no better way to spend your days than manually constructing SEO elements in your handcrafted pages and are constantly checking your analytics to see if the last set of changes shaved off a tenth of a percentage point from your bounce rate... then skip WordPress entirely (if SEO is the only reason to install it) as it won't be doing anything different from what you are already doing.
