I've posted here before that I'm discovering lots of useful things in Sonar that I simply didn't know and I wonder what else I'm missing that you all may use.  If there's another list like this please feel to direct me too it.
 
What are the top five tools in Sonar that really improve your workflow?
 
At this point, these are mine (not necessarily in order).  I realize it's six...
 
Track templates
Automation lanes
Step sequencer
All window management stuff
Keyboard shortcuts
Prochannel
 

In no particular order:

• Multi-dock (MD)
• Smart Tool
• Inspector (I've seen it described by someone else as a "right click menu on steroids") - oddly even though I love the MD I float this window center screen and toggle on and off.
• Automation Lanes are most welcome and well implemented
• This one is hard to describe: It isn't a tool, it is the overall workflow and integration of all the tools. Kudos to the Sonar team at Cakewalk.

So there you have it, my fab five.
 
Regards,

Multi-dock - at least for 64 bit effects/synths.  Nice way to keep everything tidy and mostly at a mouse clicks reach.  I have my dock on a second, smaller screen, along w/ the browser window stretched onto the left side.  Very nice work flow.
 
Prochannel.  Since I'm vested in it as far as the plugs, I seldom have to go outside of it for fx.  The EQ could use an expand function, but then I figure I can just use my ears.
 
The smart tool is good, except when it ain't, then it is a pain.
 
Those are the one's that pop out.
 
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Multi-dock - at least for 64 bit effects/synths.

I don't know if it matters but it is possible to dock 32bit plugins by their VST header. To access a 32bit plugin header, open the plugin UI holding the SHIFT key. The VST header is usually located behind the plugin UI. While the UI won't dock the header will and the it is possible to reopen the UI from the header.

You've already mentioned a bunch of my favorites, but let me add...
 

• Auto-zoom. That has saved me hours.
• Quick Grouping. I use it all the time.
• Clone track. If you're into hex guitar, it's a major time-saver. (Well, someone else must be into hex guitar!)
• Does the Velocity MIDI plug-in count as a tool? If so, add that to my list.
• Screensets!!
• Totally agree about the Pro Channel. The more I use it, the more I like it.
• V-Vocal and AudioSnap. I still don't understand why they don't give me problems...but I'm not going to say that too loud, just in case they hear me and decide to act up. However, I only use these manually to do spot correction of out-of-tune or out-of-time notes, so I don't stress them out too much.

I have mixed feelings about the Smart Tool. For MIDI editing, it's kind of a pain because I need to do so much "gear shifting" with the Function keys. I find it much more effective for audio.
 

Screensets (this is the main reason why I upgraded to X2)
PRV (this was what attracted me to Sonar 6 originally)
Drum Maps (room for improvement, but I'd hate to live without them)
V-Vocal (even though I don't use it often it has always worked well for me)
Per-track EQ (always using it)

Hard to put together a list because its the way things work together that matters. But I think overall the midi editing and recording is the main thing for me because 95% of my work is with virtual instruments. I also like the fact MIDI and Audio tracks can be kept well separated.
 
I looked at both Reaper and Studio one when X1 was released and did not like the MIDI implementation in either of them.

D
SHIFT-D
 
Is that five?
 
Oh, OK...
 
Smart Tool (could be a little smarter though)
ProChannel
Folders
 

My fayours:
 
pro channel effects
multi-dock
quick Groups
screen sets
browser
 
and this forum
 
 
 

Secondary snap
X-ray
CAL (legato, double, etc.)
Center view (forgot the exact name but it's in the shortcut key list)
MultiDock with "Lock Content"

These aren't actually my top 5 but I thought maybe the OP doesn't know these yet.