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Do you want a reader or a pad/tablet? Reading on e ink is significantly better than an lcd screen, but if it doesn't bother you, go for it.
Personally, I just want a reader. I can use my phone or laptop if I need something else. I have the Nook and I love it. It doesn't have a file tree system, but once you root it you can make collections by tags using calibre. It supports epub and pdf, which are what most libraries and a lot ebook stores use.
It does most of the things you want or would like. There are lots of add ons once you root it with the nookdev software. I am not sure you will get any reader with outstanding pdf support. Even with the Kindle DX, a pad would give you better results. But if it is text, I don't think you'd be disappointed. I have pds with txt and some graphics and they look great, imo.
Must haves:
+- outstanding .pdf support
x collections or tags- ability to set up and browse by file trees
+- 6" eink screen
+- sdhc support
+- durable/reliable product
+- that the reader not be heavily invested in DRM
+- under $300
Would be nice, but not necessary, to have:
+- wifi
x only 2 but the most common - a wide variety of formats supported
+- touch screen
+- the ability to annotate
+- linux-based OS
+- web browser / html support
+- lots of customization options
+- support for apps
+- solid ergonomics
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