I was audited last year, and it was hideous. This happened even though I hired a full service accountant as soon as I received my book contract to do all the financial thinking for me. I believed I was doing everything right, and honestly, I'm still not sure why I was targeted for the very extensive audit I received (and I mean, extensive--student loans, the sixty dollars of interest I received from my bank account, car, office, research, etc.) Every field that could be examined was examined. My accountant had to have a sit-down meeting with the auditor to comb over everything, and for anything they adjusted, they added on fees. I paid several thousand in just fees to the IRS, not even touching on what my accountant needed to be paid for his time.
I guess I'm just happy it occurred very early in my career. The year audited was actually the very first year I made enough money to need to pay taxes.
That said, I've definitely adjusted how I organize everything. I've always been very diligent about saving receipts, but those suckers tend to fade. To avoid such problems in the future, I bought a NEAT scanner and I've been scanning in all my receipts as I get them and always saving them to USBs in case my computer goes kaput. NEAT lets you compile them all into separate PDFs documents. I've always kept Excel documents of my expenses, but I'm also going to put together a calendar cross-referenced with my credit cards to track what day I was here, what day I was there, mileage, etc. (I didn't bother tracking or deducting mileage in the past, but after paying thousands to them, I'm certainly going to deduct anything I legitimately can in the future).
I'm also going to switch to an accountant who covers for free during a potential audit. Since I still am uncertain what drew such thorough attention to me the first time, I am wary about the possibility of it happening again. The fact is, there's generally always some way to pick apart a return if it's examined closely enough.
So, tldr version: NEAT scanner to capture receipts before they fade and sort to categories, Excel spreadsheet to sort to categories, and calendar.