I am wondering if anyone knows of an app where you can open files (pdf/doc/ppt), and add notations to them either hand written or typed? It would be ideal if the app could get the files from dropbox and save them to there. Thanks.
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An app to notate files?
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Have you seriously never heard of Goodreader? It is posted about here all the time and is frequently in the top 10 in the app store.
Haha, no. I must have just skimmed over it, since I routinely look for new apps.
That is, of course, exactly what I need. Buy buy first $10 bucks from gift card I got with Macbook Pro. Grabbed both iPhone and iPad versions. Thanks. This will make school so much easier.
They sure fooled me! While it says it works with all kinds of files, you can only actually annotate PDF files.
Unfortunately, you need to purchase another app to convert your non-PDF files to PDF. Check out Save2PDF or PDF Converter.
I am a big fan of PDF Expert because it lets me sign my PDFs. It fits into my workflow very nicely. 
I highly recommend PDF Converter, which I use for web pages (Safari only). Unlike Save2PDF, it *always* works, even on https pages. Save2PDF must be running in the background. Since Apple cuts off an app's ability to run longterm, you're never quite sure if it's still working. In contrast, with Readdle's PDF Converter installed, I just place my cursor in the address bar, situate it in front of the http, and type pdf (pdfhttp:// -address -). Tap Go on the keyboard, which auto-tosses you into PDF Converter. Click the Convert button. Within seconds, it's done.
FYI Workflow: After conversion, I tap PDF Converter's arrow to "open in ..." Readdle's PDF Expert. I add comments/notes, which ARE searchable via EagleFiler, but NOT Spotlight. Expert allows me to easily rename the file if desired. Also let's me stash the file in the "To Import" folder of my desired EagleFiler library, the entirety of which lives (nicely!) within DropBox. Since I have EF Smart Folders, which look for the keywords most frequently used in my PDF comments, the organization of such iPad-secured files is pretty much automatic.
Really has made research chores MUCH easier! (Don't know any of the devs; just passing on my experiences to spare interested folks aggravation (Save2PDF) and share a "hey, this combo works!!" discovery.)