Apart from the basics (Apple mail and Chrome), here are my top 5 in terms of usefulness, not necessarily most used...
1. Activity Monitor. I love this little app to death. Great to know what process is eating my CPU cycles or using too much of my limited RAM. I pretty much have it open 24/7
2. SMC fan control. A lifesaver for my lap

3. Photoshop. Yep. Gotta edit those pixels!!
4. Disk Inventory X. A beauty of a free program, if you want to know what is eating your hard drive space away...
5.
Adapter. A quick and easy file converter, works fast, and is free!
Now my top 5 "most used" (not counting any of those above). In no particular order...
1. Microsoft office
2. Spotify
3. EAGLE PCB design software
4. Aperture 3
5. Arduino IDE
And here, for absolutely no reason other than I can is a list of mac apps I would happily have pre-installed on macs if they could be
Disk Inventory X
SMC fan control
Adapter
Handbrake
VLC
Audacity
Time Lapse assembler
Microsoft Office Suite
Adobe Suite
Arduino IDE
EAGLE
Google Chrome
VMWare Fusion