Yojimbo is nice because it has a modern, clean interface and it's simple to get information into it. It also doesn't do too much, other than tagging files and serving as a searchable repository for them.

DTP does far more but has a dated interface, feels clunky as an Human-Machine environment and can be daunting because it has a steeper learning curve. DTP 2.x should be the mac-daddy of info managing applications after Leopard hits the scene.

Also, Scrivener just introduced a neat feature called the scratch pad. It is a floating and dockable window that accepts notes, links etc and can send them to an internal scrivener document of your choosing.

I also forgot to mention Quicksilver. It is indispensable to me. I am beginning to explore it's file tagging abilities and will likely use it to integrate the aforementioned applications as a means to facilitate my workflow. QS has a steep learning curve but it is well worth it, IMO. I am only at the beginning and I'm already seeing benefits.

Merlin also loves QS. Check out lifehacker and the appleblog for more tutorials on QS. You won't regret taking the time.

Find what works for you, the way you like to work.

cheers

:)