Wipe Data, Not Software
First of all, the direct answer - yes, you can wipe data without loosing your apps. This will not give significant if any at all improvement in mac's performance, though.

To do it, just clean your home folder, but be careful not to remove the following folders:

~/Applications
~/Desktop
~/Documents
~/Downloads
~/Movies
~/Music
~/Pictures
~/Public

Also, you can remove all contents of all folders except ~/Applications to keep applications intact.

Now let's move to actions which will actually help to improve the performance.
Macs get slow for a reason. What's good about OS X is that you can always see this reason.

Open ActivityMonitor application which is within Utilities folder and sort the list by "% cpu" in descending order (two clicks onto column header). Now you see which applications consume most of CPU power. Probably the violator will be there. It is up to you whether to uninstall these apps or to keep them.

Next, open Console, which is still within Utilities and look in All Logs section. If you see some king of logs dropping constantly with high speed that's another possible violator.

Next, open Disk Utility and perform Check Disk and Check/Repair permissions. Sometimes helps.