Most of the commands available on the main toolbar and the collection toolbar have keyboard shortcuts associated with them. The editor box where you can edit the text held by a clip recognizes many additional text editing keyboard shortcuts not listed here.
The system-wide hotkeys that you can configure in the Hotkeys Preferences are also not listed here.
Ctrl+N New AceText Collection
Ctrl+W Close AceText Collection
Ctrl+O Open AceText Collection
Ctrl+S Save AceText Collection
Ctrl+P Print AceText Collection
Shift+F5 SequencePaste Up
Ctrl+F5 SequencePaste Down
F8 AceText Editor
Ctrl+F8 AceText Tower
F12 Always Visible
F11 Word Wrap
Shift+F11 Line Numbers
Ctrl+F7 Automatic Capture
Alt+F7 Auto Append
Shift+F7 Auto Split
Shift+F4 New Folder
Ctrl+F4 New Subfolder
F4 New Clip
Shift+Ctrl+O Create Clip from Text File
Ctrl+D Duplicate Clips
Ctrl+M Move Clips
Shift+Ctrl+Up Move Up
Shift+Ctrl+Down Move Down
Shift+Ctrl+PgUp Move to Top
Shift+Ctrl+PgDown Move to Bottom
Ctrl+G Merge Clips
Shift+Ctrl+G Split Clips
Del Delete Clips
Shift+Ctrl+X Cut Clip to Clipboard
Shift+Ctrl+C Copy Clip to Clipboard
Shift+Ctrl+V Paste as New Clip
Shift+Ctrl+R Read Only
Shift+Ctrl+L Lock Collection
Ctrl+F Focus Search box
Ctrl+F Find Next (if Search box has keyboard focus)
Ctrl+F3 Find First
Ctrl+F6 Find First Clip
F3 Find Next
F6 Find Next Clip
Shift+F3 Find Previous
Shift+F6 Find Previous Clip
F2 Filter Clips
Alt+F3 Replace Current and Find Next
Shift+Alt+F3 Replace Current and Find Previous
Ctrl+Alt+F3 Replace All
Shift+Ctrl+F Search Options
Alt+F2 Find Duplicate
Ctrl+F2 Highlight All
Ctrl+I Incremental Search
Shift+Ctrl+R RegexBuddy
Shift+Ctrl+D Duplicate Text into New Clip
Shift+Ctrl+M Move Text into New Clip
Ctrl+X Cut Text
Ctrl+C Copy Text
Ctrl+V Paste Text into Clip
Shift+Ctrl+S Save Text
Shift+Ctrl+U Upper Case
Shift+Ctrl+L Lower Case
Ctrl+Q Straight ⇒ Smart Quotes
Shift+Ctrl+Q Smart ⇒ Straight Quotes
Ctrl+/ Toggle Comment
Ctrl+T Trim Whitespace
Shift+Ctrl+T Trim Whitespace from Paragraphs
Ctrl+Tab Activate the next tab
Shift+Ctrl+Tab Activate the previous tab
Alt+1 through Alt+0 Activate tabs 1 through 10, counting from left to right
F9 Focus Editor
Ctrl+F9 Focus Clip Tree
Ctrl+Arrow Up Select previous item
Ctrl+Arrow Down Select next item