Number of files
If you are just starting out with digital photography this will not be a problem for you, but as time goes it will silently grow to something that needs handling. I have been using digital cameras for almost 10 years now and as a consequence I have gathered a few photos. At last count I had more than 40 thousand photos. My photo collection has so far only undergone one transformation (a split to two hard drives so I know which photos are properly backed up and which ones are not). In other words I, quite by accident, made a good decision on how to store my photos and now it scales fine. When you have a couple of hundred or a couple of thousand photos it is easy to handle. 40 000 is a different story.
Structure your files
I will here post my structure as I think it is a good structure that lets me easily find photos. What I do is that I create one directory for every year, under that I have a directory for each month . Under that I have a directory for each day. I do not create empty directories.
Name your files
I have my files named as follows yyyy-MM-dd-hhmmssUID.jpg for example 2008-03-15-145312AA.jpg. Since your photo contains all this information you do not have to do anything yourself. When I take pictures off the camera I have a program that looks at the EXIF of the file and extracts this information and rename the file in this format. My program also creates the directory if needed. Which program? I wrote it myself, but there are several program around that can do this. If there is interest I can put my program up, it is not fancy, it does the job, nothing more.
By having this structure I can very quickly find photos if I know the date, or even a range of possible dates. Also it is easy to move files away to a different location should you need to. You can for example grab all photos from 2003 and stick them on a different computer if you need the space.
Backup your files
I know this has been said before but considering how lazy (I may even go as far as saying 'stupid') some people are, it is worth repeating. Since you have no negative, once the photo is off the camera and your card cleared you have no other copy of your photo. YOU will need to make sure you have additional copies. I put all photos on two computers (I make the copy at least every week, as part of my regular backup). This ensure against hard drive failure. If you have not done so, get an external hard drive to store your photos on. When I reach 4,7Gb I make a dvd with all the photos and store the dvd away from the computers. What kind of backup routine you need depends on your photos. Keep in mind that your backup medium may be attractive to thieves if they break in. Possibly you want to make two dvd's and send one disc to your parents/sibling/friend so you have a copy that will not be stolen or damaged during a fire. If you have not already devised a backup plan do so now! It IS important. (don't believe me? delete all your photos and see how you feel..)