By default, Haiku's option key, to invoke commands from menus for example, is not the usual CTRL key, but ALT instead. This has historical reasons, because the BeOS was inspired somewhat by MacOS. After you get used to it, it actually feels better as e.g. ALT C and ALT V is reached more conveniently on the keyboard and these commands seamlessly integrate into the bash shell of the Terminal, where CTRL C quits the running process.

In any case, you can switch to the maybe more familiar CTRL key in the Menu preferences. The user guide will always describes the default configuration with option key being ALT.

General shortcuts

Here's a table of many of the most commonly used shortcuts that are always available, even if there isn't a corresponding menu:

ALT Fx		Switches to Workspace X (Fx is the function key corresponding to that workspace).
CTRL TAB		Hold down to bring up the Twitcher.
CTRL ALT DEL		Opens the Team Monitor.
ALT ESC		Enters the menu bar (leave with ESC).
ALT C		Copies the selection to the clipboard.
ALT X		Cuts the selection to the clipboard.
ALT V		Pastes the clipboard's contents.
ALT W		Closes the current window.
ALT Q		Quits an application.

Shortcuts for Tracker navigation

Additionally to the general shortcuts, here are some more for navigating with Tracker:

ALT ↑		Opens the parent folder.
ALT ↓ or ENTER		Opens the selected folder.
WIN		Holding it while opening a folder will automatically close the parent folder. This also works when navigating with the mouse.
right MENU		Opens the Deskbar menu (leave with ESC).
ALT Z		Undo last action. The undo history is only limited by the available memory. Note, this only works for actions on the file itself, changed attributes and permission settings can't be undone with this. Also, once a file is removed from Trash it's gone for good.
ALT SHIFT Z		Redo the action you just reverted with ALT Z.

Shortcuts in Terminal

ALT N		Opens another Terminal session in a new window.
ALT T		Opens another Terminal session in a new tab.
ALT 1, 2, 3...		Switches to the corresponding tab.
ALT G		Switch to the next Terminal window.
ALT +, -		Increase/Decrease font size.
ALT ENTER		Enter/leave fullscreen mode.
SHIFT ↑/↓		Scrolls the Terminal output up/down one line.
SHIFT PageUP/PageDOWN		Scrolls the Terminal output up/down one page.
TAB		Tab-completion. After entering a few letters, press TAB once to auto-complete a filename or path. If there is more than one match, it stops where the name starts to differ and you have to provide some more letters to further distinguish them. You can also press TAB twice to have all matches listed.
↑/↓		Moves up or down in a history of all previously entered commands.
CTRL R		Bash history. All the commands you enter are stored in the file ~/.bash_history. Press CTRL R and start to enter a command and you'll be provided with the first match from the bash history. Keep pressing CTRL R until you find the right command line and press enter to execute it.
CTRL C		Stops the currently running command.
CTRL D		Closes the current Terminal session.

Other key combinations

You can add or remove items to/from a selection by holding down a modifier key while clicking on a entry (or file in case of Tracker).

SHIFT		This will select everything between the first selected item and the one you click on.
ALT		Adds or removes the item you're clicking on from the selection.

In a Tracker window, if you just start typing, Tracker scrolls to and selects the file that best fits your incremental search. If there's no file starting with your typed letters, files that contain the search string anywhere in their name or other displayed attributes are selected. This search is not case-sensitive.
The letters you type appear at the bottom-left, where normally the number of items is listed. After a second it reverts back and you could start a new incremental search.