Don't try to be too fancy with organizing. Although there is the ability to create new parent folders and subfolders on import-in my experience I have found that this can create problems because if you forget to update the folder name you can easily wind up with photos going into the wrong folders. Stick with parent folders of years and subfolders with dates and a description.
Don't go behind Lightroom's back. You can move files and folders anywhere you like but you need to do it within Lightroom. If you just go directly to your hard drive and start moving files and folders Lightroom will not know the new location and will show it as "missing".
Use Collections to sort through images. Creating a collection is an easy way to sort through your best images, cull images from a job or vacation.
Use Smart Previews. If you are using an external drive to store your images you will notice that when you unplug the drive the files are now described as "offline". A couple of versions ago Adobe introduced "smart previews" which generates a smart preview on import that will allow you to work on the image when the hard drive is not plugged in. This allows you to leave your drive at home and when you plug the drive in it will update the files with any changes you may have made.
Delete files on a regular basis. Staying up on removing images that aren't any good is key to keeping and orderly Catalog. Think of your Lightroom Catalog like any other space in your home, the garage, basement or attic-if you keep letting things pile up it becomes and unruly mess that no one wants to deal with. There is no time like the present to do some housekeeping.