Here's the deal, it's not you, it's just many people with little experience think that.
Just like that other guy said, Hard Drive usage shouldn't affect your machine's speed at much at all, except when you use a program that has MANY files stored that it needs to load, such as when you first start up 3DS Max.
Your computer actually just starts lagging up when a lot of your Ram space gets used up. If this is the case, I advise you to go to a hardware store and buy a new Ram to add on to your comp's current memory. Ram's aren't that expensive, they range from 50-150 dollars, depending on the brand and how much space it holds.
If it's not RAM problems, it's most likely CPU. Most standard prebuilt desktops today come with a 2.4 gigahert processor, which is indeed fairly fast. laptop(that cost around 500-1500 dollars) CPU's can range from 800 Megahertz to 1.8 Gigahertz. This just means..... Your comp isn't invincible. It will lag up if you Run more apps that it's able to run, or if you run an app that eats up your CPU.
One way to make the startup process faster is by disabling useless processes and services. Just click start---> Run, in run type msconfig. a new window should pop up. click the startup tab, and disable all processes, and rechecking all the ones that you like. then go to services. DO NOT DISABLE ALL. just disable the ones you hate.