Evernote
Evernote is absolutely wonderful! It is a note taking device that is free to download and automatically syncs all of your notes between any device that you have (laptop, smart phone, Kindle fire, etc). In Evernote, you can create different notebooks in which to categorize information. For example, here is a screenshot of my current Evernote account:
As you can see, you can create either "stacks" of notebooks which incorporate multiple notebooks into a category, or you can create individual notebooks which have to do with certain things.
My advice on using this tool during college applications would be to make notebooks for scholarships (in that notebook, make a note for scholarships you need to apply for and scholarships applied for), potential schools, major research, tests signed up for and scores, and a notebook that has all of your potential resume material. When used right, Evernote can really help you out!
A Physical Notebook
Not every organization strategy has to be using fancy online tools and technology. Sometimes a simple notebook works the best. Create a colorful, fun to-do list for yourself and put it in the front of your notebook categorized by tab, then put dividers in your notebook and print off all of your completed applications and essays and put them in your notebook. In case if something goes wrong with the technology, it is always a good idea to have a hard copy of everything you do.
Post-it Notes
Post-it notes are a surprisingly helpful reminder tool that most people feel like they don't need to use. Trust me: once you start having multiple applications to complete, you will appreciate the reminder. When you have a deadline coming up, jot down the name and deadline on a post-it note and stick it in a place that you look every day (my advice would be your bathroom mirror). This way, you will have a short reminder every morning and evening at the least.
Cappex/Zinch/Other college planning website
I've written briefly about these websites in some others posts, but just to refresh your memory, Cappex and Zinch are two of many free online college planning services and scholarship searches. Be sure to check them out!
College applications become a lot less stressful when you have a good system to manage them. Never underestimate the power of multiple reminders (phone alerts, post-it notes, etc) and get started early on carefully classifying your information. In the long run, getting organized can really help you to be the most efficient with your time and with your applications!
Best of luck!