Software
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Documentation
A GitHub wiki (Gollum wiki) is a personal wiki using Markdown syntax with some added sugar. The best thing about them is that they do not force you into a specific folder-structure. You organize your files, Gollum links them together and displays it. If you have a GitHub account (which you should) you can edit your wiki from the web and even share it with the world if you want to.
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PDF Library
Papers (v2), though I am not particularily fond of the direction this app has taken, I find Papers (v2) to be a great app for searching databases and organizing PDFs.
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PDF Reading and Annotating
PDFExpert / Remarks (no longer available) on the iPad. Preview on the Mac together with the PopClip PDF Highlight extension for quick highlighting (Skim if Preview is having a bad day).
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PDF processing
My very own Mac app, Highlights, for extracting PDF annotations to Markdown. I save the annotations in my Gollum wiki with a link to the PDF at the bottom.
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Task management and lab protocols
TaskPaper (for iPhone and Mac) is a great tool for combining notes and tasks. I have used it for 3 years now and it is still the only solution that makes sense for what I do. The only problem is syncing issues. I work in a lab with very poor cell coverage and this can cause duplicates or in worst case loss of entries (the worst!).
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Note taking
Plaintext notes go into nvAlt on my Mac and are synced to Taskpaper on my iPhone. Images are captured on my iPhone and go to Evernote for OCR. For conferences and lectures I use Notability on my iPad.
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Diagramming and simple figures
OmniGraffle is the most intuitive drawing app I know. I have made figures for all kinds of presentations and papers using this app.
Hardware
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iPhone 5
My primary computer for both work and home. The only computer I have with me into the lab and the one I use the most for browsing/twitter.
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Macbook Pro Retina 15"
My workhorse and pixel paradise.
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iPad 3rd generation
My PDF annotation tool of choice and travel computer.