There are 2 things to consider before you choose one of them, which are:
- Site Security.
- Site SEO.
If you need a tight security, then you should go to personalized subdomain, there are several things that will tightened your site security when you choose personalized subdomain, which are:
- No Google Indexing. You can avoid google indexing your private client site, and you can safely index all of your www site without worrying your system will be compromised.
- Avoid site hacking from viewing your robots.txt. You can safely disallow google from indexing several of your pages or directory structure, but someone can easily peek into your robots.txt and find something precious there.
If you prefer security than search engine optimization, then you can choose personalized subdomain, but the implementation is a bit tricky, don't use dns to add a cname or an a record to your subdomain, simply add an a record for *.yourdomain.com, and you can safely manage your subdomain with vhost from your web server, so no one can enter the subdomain without knowing the exact name of it first.
If you need to optimized you site rank in search engines, you can use this method. You can prohibit some places to be indexed by search engine with robots.txt, and hopefully no one knows where it resides. Also you can have your site rank higher than the previous method, because all of your client visit your main site, rather than their own subdomain.
I personally choose the first option, since I cannot afford loosing some pages to be unintentionally indexed by search engine, or someone somehow found my robots.txt. If I need SEO more than ever, I can simply create a blog for the company and have it indexed, that would attract more people and have a higher unique visit, and increase rank, rather than risking my system easier to be compromised.