There are several reasons why your computer could feel slower to day than it did when you first bought it.
1) startup speeds slow down as you add more programs and utilities to the login items list. Open your system preferences and look at the Accounts tab - login items. There may be things you can remove to speed up the boot time - but be careful because you may need some of them there for certain programs to work as expected
2) as users start using their computer with more confidence and authority the small amount of RAM their computer came with can become overwhelmed by the 10 programs they now launch regularly. Open up the Activity Monitor and see how much memory your computer is using. Pay attention to the swap outs and swap ins. Lots of activity there could mean it is time for more RAM.
3) as you begin adding more movies, tv shows, and music to your collection the very large hard drive become full. You should, in general, keep at least 15GB or about 10-15% of your hard drive space free (whichever is smaller). Many programs need to create their own temporary files, swap files, and caches - not including what the operating system itself does - so leaving some breathing space is a good idea. There are also utilities that can clean various OS and application cache files which will reclaim space, though as you begin using the computer again they will be rebuilt.
4) along with having enough hard drive space is disk fragmentation which seems to be what you are concerned with. I left it for last because it is, generally, the last thing we Mac owners need to be concerned with. Unless your hard drive has become overly full or you deal with video or audio files which you load up the drive with and then delete later, you probably don't have much to worry about. The Mac defrags the hard drive pretty well on its own. However, if you think this is the issue that is causing your slowdown, the easiest way to fix it is with SuperDuper! (or carbon copy cloner) and a second hard drive. Both these programs perform file level bootable backups of the hard drive. So as the files are copied to the secondary drive they are all laid down without fragmentation. They aren't optimized, which is another story altogether, but tests I've seen with optimized vs unoptimized drives haven't shown me a significant enough difference for the ordinary user to make the cost of the software worthwhile. Not saying there's no benefit, but most of us don't really need it.