Hi! I have both JKDefrag and PerfectDisk on my computer. Here are some of my thoughts on both programs.
Areas where PerfectDisk is better than JKDefrag, in my opinion:
1) PerfectDisk has great boot time (aka offline) defrag which makes it easier to defrag some unmovable system files that cannot be moved while Windows is running.
2) PerfectDisk optimizes boot files according to layout.ini file which may lead to faster Windows startup. However, differences in boot times between JKDefrag and PD are not so large on my computer (after PerfectDisk my PC boots only about 4 secs faster than after using JKDefrag, from what I've measured).
3) PerfectDisk tries to reduce future file fragmentation by consolidating free space and putting frequently modified files close to that free space. So, when those frequently modified files grow in size, they won't become so fragmented since they are followed by large chunk of free space.
Areas where JKDefrag is better is PerfectDisk, in my opinion:
1) I find that JKDefrag places files in a way that leads to better general computer performance than PerfectDisk. JKDefrag organizes disk into 3 zones: Directories followed by some free space, then regular files followed by some free space, and SpaceHogs (large files, archives, MP3s, rarely accessed files, etc.). Because of these optimizations, regular files and folders can be accessed quicker leading to a better overall performance.
I personally use PerfectDisk for a boot time (offline) defrag only (when my unmovable system files get fragmented), and JKDefrag for normal defrag.
Best,
igt