First of all, the CPU's your machines have are probably a few CPU's combined into one (more physical cores). It is even possible that each physical core has a few logical cores.
Second - the usage on your laptop may not be maxed out, but if the program is single threaded then it can only use one, and only one core, not more. This means that if you have four cores, and windows task managers shows a 25% CPU usage on one program, then it means that one program uses the maximum speed of one core, it can therefore not perform faster.
To take an example, my i7-3xxx processor has 4 physical cores. Yet each core has two logical cores, which means I have a total of 8 cores to my disposal. Windows then can assign any program execution to any core to maximize efficiency. If the program you run can only use one core then Windows can not do anything about it (or any other OS as far as I'm informed) other than let the program execute at the maximum speed of one core.
Third - RAM and CPU usage can be almost 0%, this does not mean the the hard disk is not in use. Even on newer hardware hard disk are almost always a bottle-neck. When the hard disk is being used at maximum the total performance of the computer seems to always decrease. A hdd being used at maximum especially hits the applications that do like to move data around. Application's that don't use HDD that much still will get slower but are not being impacted at the same rate as apps which require the HDD.
Also, tip, if any of the above reasoning does not apply then it's just because your desktops' hardware is better. Computers are complex and every parameter does matter - ram speed, ram size, bus speed, cpu cache(s), cpu speed, supported cpu instructions, hdd rpm, hdd speed, software configuration, background processes, etc..