Things I found helpful while planning (and conducting) my recent research trip:
Evernote: This is free-form (and free!) note-collecting software that syncs across all your mobile devices. I put together a notebook with weblinks, snippets of text, and lists for all the stops I planned to make, including libraries, my hotels, courthouses, etc -- and they were all available on my phone, my iPad, and my laptop, even when I didn't have internet access. I was also able to share it with my mom, giving her the info she would need if she needed to track me down (and my phone didn't work for some reason.) I find I'm using Evernote more and more as I learn more about it.
Google Maps: I made a custom map with pins for every library, cemetery, courthouse, hotel, restaurant, and symposium location I thought I might stop at. It was very helpful for planning my days. It would have been more helpful during my days if A) I had internet access everywhere and/or B) there was a way to sync it to my car's navigation system.
TMG: The genealogy software I use, The Master Genealogist, has the option to print lists of all the events that meet a given criteria, sorted however you like. I made event lists for every event that took place in the counties I was visiting, sorted by city, which helped me figure out who to look for in probate indexes, deed books, and cemetery indexes. I even had a couple of addresses of residences and businesses to check out in hopes of finding original houses, businesses or churches (I found a couple of possibles).
A plain spiral-bound notebook: I still find this the best way to take notes on the fly -- you can schlep it around a cemetery, use it to hold down grass while you take a picture, and use it as a plate for your afternoon M&M break. Plus, you can use it anywhere, anytime, without worrying about power or dropping it (or sweating on it -- those cemeteries were hot!)
This article by Thomas MacEntee: I didn't use all of his suggestions, but it was a good way to start focusing my thinking.