I use Devon Think Pro Office for all things needing to be in a filing cabinet (bills, credit card statements, scanned in - DTPO is great for that, and lots of other long term items to be filed away).
I've used Thoughts to store on-the-fly notes, full or part images of web sites, anything else that is "temporary" or needs to be accessed frequently.
I've begun testing Eagle Filer, and while it doesn't seem to be as good for jotting down notes as Together, it does support MetaTags. I use Leap and Tags for tagging files, and it's now important for my filing apps to support these tags. Together and DTPO do not, instead they support their own version of tags. The tags are important for files and other content that don't fit into a folder-like hierarchy, which is why EagleFiler's support of metatags looks attractive. The way I use DTPO, tagging is not important.
Oh, and I use PersonalBrain for thoughts that are interrelated with other thoughts. I use that for information that I may not be able to find if tagged, since I may not be looking for a specific item or I may have forgotten what the item is about (hence I can't do a search).