I use the good old gray matter to keep track of plot and characters. If things get to complicated for my own brain to keep track of, they are probably to complicated for the reader too.
For notes and the manuscript, I still use the same old word processor I used for my papers back at Uni. If I had to use Microsoft Word, I'd be going nuts within a week.
Other than that, the most important thing to use is a USB stick where you keep different versions of the text and all the notes. I carry the stick in my pocket whenever I leave the house (in case it burns down while I'm away) or on my bedside table at night, in case the house burns down at night and I have to grab the stick and jump out the window. After each finished Chapter, I copy the lot onto a CD, and whenever I am visiting my parents or in-laws, I deposit the newest CD at their place in case some other unforeseen catastrophe happens at my place.
Did I mention my husband works as IT storage consultant and has been drilling me for years that anybody who loses important data has only himself to blame for?
Oh, and of course a thesaurus, and -- since I am not writing in my native language -- a dictionary of collocations and a German-English dictionary. The collocations dictionary is a real book, the others online and on my computer.
P.S. Don't waste too much time on gadgets, just write the novel!