Yes. Several smaller (4" or 5") case fans mounted in a sealed case will cool your entire system better than one big fan blowing into an open case. One fan mounted low in the front blowing outside air in, and the other fan mounted high and in the back (I cut a hole in my case above the CPU) will work very well.
I tried the desktop fan approach, but it gaussed out my monitor. Made it flicker and shake, and on the other monitor it distorted the picture and fucked up the colors.
Don't use a desktop fan unless it runs on DC. AC does the afore-mentioned gauss action.