How do you execute a query in Sequel Pro?

Use ⌘+R to execute the selected Query.

Alternatively, use the dropdown that appears at the bottom right of the query editor and select Run Current or Run Previous depending on where your text cursor is.

Based on Keyboard Shortcuts:

Run all queries ⌥ ⌘ R

Run current query or selection ⌅ or ⌘ R

Use the drop down button on the right side, underneath the textarea.

Should have the following options:

• Run Current Query
• Run All Queries

Came here to find ⌘ + return to execute a query (like MySQL Workbench).

Found that I can map using mac Key bindings with the names of Run Current Query and Run Previous Query.

If you want to do it via terminal it would be (untested):

 defaults write com.sequelpro.SequelPro NSUserKeyEquivalents '{
        "Run Current Query" = "@\\U21a9";
        "Run Previous Query" = "@\\U21a9";
    }'

Note: you may have to restart the app.