I am a PhD student as well. I own and have tried numerous applications for note-taking, writing and information management. I've settled on Scrivener for basic writing. It allows you to structure and reorganize your writings very easily. There is a minimal learning curve compared to something like Word and it's received rave reviews from nearly everyone who's given it a chance. Highly recommended.

I use Safari to search my library's EBSCO database. I will usually batch export (download) the citations and batch email pdfs of interest.

I use Bookends for Bibliography management and creation. It's a solid application with stellar support from Jon at Sonny Software. The UI is a tad dated but it works quite well and integrates specifically with Mellel, Nisus and Word. It also plays well nearly any other WP or text editor you like.

I use a few applications to manage my information gathering. Currently I use Yojimbo to capture generic web pages and quick notes on general, non-academic topics. I am also evaluating eagleFiler for the same.

I primarily use DevonThink Pro as my personal research database when writing papers or resarching for a weekly discussion.

In addition, I use currently Papers to search Pubmed and grab available pdfs of interest.

A sample workflow may look like this:

Papers- perform a Pubmed search and import references of interest. Grab available pdfs in Papers as well.

Export references to Bookends.

Bookends - locate and attach local pdfs to imported references.
Optionally, use Bookends to perform pubmed searches as well and to import available pdfs and automatically attach them to the appropriate reference. Import references from EBSCO. Find and attach local pdfs for said references.
I also copy the full citation information into the comments field of each pdf in the Finder. It only takes a few keystrokes and facilitates using DTP for final research.

DevonThinkPro - I'll import all attachments (pdfs) from the Bookends attachments folder. I use the Pro Office version so if any pdfs are images (missing searchable text) I'll OCR them after import. Again, you can batch process them so it's only a few keystrokes.

After all papers are imported I start searching for topics of interest and begin the reading and note taking process.

Scrivener - I use this to take notes on notecards or in individual text files from papers in DTP. You can add citation information to your notes so Bookends can create a bibliography automatically after you finished and you export the paper for final formatting.

In DTP, I may highlight text I've used as a reference as well as label the individual pdf with a specific color for later reference or in case I'd like to review the text or other sections in the same paper.

My workflow is still evolving and needs tweaking here and there but I hope this is helpful.