I have been developing a web application which has many documents (.pdf format) which must be embedded on the site. After doing a little research, there seem to be many "services" and/or "libraries" which allow the same functionality as the <object> tag combined with an Adobe Reader plugin. Some examples include Crocodoc.com as well as PDFobject. Although, I will admit, a side by side comparison of these two SaaS, Crocodoc would take the lead.

It has been well known for awhile now that <embed> coding is outdated, and the best methodology for .PDF implementation is the <object> tag, in a previous discussion located here on SO.

However, one does not dispute that from a basic implementation approach of having standard-pdf bookmarks, links, and a 'table of contents', it appears that the browsers built in (downloaded, whatever...) Adobe Reader plugin provides the same functionality as one of the many plug-ins or extensible libraries provided on the web.

I would like to approach all the wonderful experts here on SO to provide an objective approach to the pro's and con's of using such methodology. Feel free to use subjective opinions, but please back them with facts and a well researched answer. Thank you.

Edit

After being approached on the topic that subjective answers are not suitable for StackOverflow, please keep in mind any subjective opions must be backed by a fully endowed, truthful basis behind any possible conclusion. Every programmer and web designer implements in their own ways because of experiences as well as pros&cons, so in order to provide the best suited answer.... "When In Rome"....