A comprehesive list of all keyboard and mouse commands.

Keyboard And Mouse

These basic key presses are typical for computer players using a US-version keyboard and may not be the same UK-version keyboards, different computer formats (eg: Mac), smart-phone users, game consoles, emulators, etc.
Definitions

LMB = Left mouse button.
RMB = Right mouse button.
Ctrl = Control keyboard button.
Shft = Shift keyboard button.
Alt = Alt keyboard button.
SB = Spacebar keyboard button.
BKSP = Backspace keyboard button.

key1 + key2 or key1 - key2 = press and hold key1, press key2, release both simultaneously.
key1 + drag = press and hold key1 and move mouse to new area, release key1.

Windows Commands (Universal)

Alt-Tab = swap window / show desktop, or
Hold Alt and press Tab repeatedly to scroll window selection, release both.
Alt-Enter = maximise screen if windowed.

Universal Commands

Enter = confirm action.
ESC = disregard action.
F1 = UFOpaedia menu.
RMB on icon = its UFOpaedia entry.
SB = pause or resume time.
0 ↔ 5 = time controls.
TAB = swap overhead or isometric views.
Alt+P = screenshot as a PCX file, 8-bit colour, 640x480 size Δ

Δ filename format XCOM0.pcx to XCOMZ.pcx within root folder. Maximum of 34 screenshots (to enable more screenshots, move old pics out of root folder to elsewhere. New screenshots filenames will be duplicates of old screenshot filenames).

Cityscape

RMB = centre here when overhead view.
O = options menu.
ESC = quit game.
Enter = highlight last message location.

Cityscape Building & Agent Selection

⊗ If multiple agents are travelling through the city on foot with multiple destinations, and if wanting to collect a few of them, LMB only on each person-icon within the cityscape. The Ctrl button is not needed since the selected agents will be all highlighted as one grouping in the Agent Tab. The limit of 13 in any temporary grouping still applies.

LMB on a cityscape building or base = displays X-Com's presence, if any (Agents and/or Vehicles).

then
The following can also use RMB instead of LMB:

LMB on vehicle name = un/highlights all agents within vehicle.
LMB on agent = un/highlight single agent
LMB+drag on agent name = highlight multiple agents.
LMB+drag on agent icon = move (all highlighted) agents: between multiple landed vehicles or to place them in the building's home-cell (home-cell = the building's name, left side if screen).
LMB on agent icon = agent inventory screen (same as right side button: "Equip Agent").
LMB on vehicle icon = vehicle equipment screen (same as right side button: "Equip Vehicle").

Top-right side of screen:

LMB:
- pink alien face button = search building ("Investigate building for alien activity")
- red building button = raid building

Tab Bar - Cityscape View

Placing the mouse cursor over any icon will display the objects name or use (tool-tip) after a short delay.

Bases Tab

Double LMB on base outline = highlight and centre selected base on cityscape.

Agent & Vehicle Tabs

Double LMB on icon = highlight and centre selected subject on cityscape.
Ctrl-LMB = select multiple (max 13).
RMB = remove from temporaty group.
Ctrl-LMB = add waypoint (onto cityscape section, see below: Cityscape Waypoints).
Shft-LMB = go to building (onto cityscape section).

Vehicle Tab

M = manual vehicle control (see below: Manual Control).
Alt-LMB = attack building or vehicle.

Using the "Go To Map Point" function: a road vehicle will never stop at its destination but will drive in circles around the general area.

Organisation Tab

LMB = (cityscape overhead view only) highlights all buildings owned (using various colours indicating relations).
LMB (multiple) = highlights each property owned.

Equip Screen

Agents

LMB on agent name = change name (maximum title width or 24 characters).
Ctrl-LMB = allows selecting multiple units.
TAB = changes attributes mini-screen.
A = switch to armor screen.
E = switch to equipment screen.

Vehicles

LMB on vehicle name = change name (maximum title width or 24 characters).
1 = Select GUNS screen.
2 = Select ENGINES screen.
3 = Select DEVICES screen.

Battlescape

View

PgUp = go up one view level in elevation.
PgDn = go down one view level in elevation.
Home = center on selected unit.

Movement

RMB (agents static) = turn to face a new direction.
RMB (agents moving) = cancel a move order.
Alt-LMB = move-to-here when destination is already occupied by another unit.
F2 = crawl
F3 = walk
F4 = run
BKSP = kneel
J-LMB in the air next to the ledge or railing = jump off/over something.
Ctrl-LMB = add waypoint (maximum 5).
LMB Click+Drag cursor over units on the battlescape = select multiple agents.

Attitude

F9 = safe
F10 = cautious
F11 = agressive

Targeting

RMB on a non X-Com unit = highlight as a target for all selected agents.
Shft-LMB = force fire at this cursor location.
F5 = hold fire
F6 = aimed shot
F7 = snap shot
F8 = auto shot

Items

RMB on explosive item in hand = set Detonate On Impact when thrown or dropped.
[ = drop item left hand.
] = drop item right hand.
' = throw item left hand.
\ = throw item right hand.
ENTER = open inventory of selected agent.
Y/N = accept/decline current timer setting on explosive device.

Cityscape Waypoints

Waypoints may be given to airbourne or road vehicles.

Switch to overhead view.
Give a vehicle a target destination (this can include "Attack" command).
Click the "Move to Destination" button (next to "Move to Building" button).
Ctrl+LMB somewhere on the overhead cityscape to add a waypoint(s), release.
The yellow line shows the new travel path.
Close the mini screen with the "X", if it appeared.

Hold Fire Forced Fire

If hold fire is used (the "X" in shot types), but something needs to be shot:

click LMB on agents weapon in their hand, white outline, click LMB on anything or
hold down shift, click LMB on anything.

Constant fire is possible if you hold down LMB.
There is an error for an agent's actions if the target was selected via RMB.

Manual Control

PgUp = Increase Speed
PgDn = Decrease Speed
Home = Increase Altitude (flying), U-Turn (road)
End = Decrease Altitude (flying) , Swap lanes(road)
LMB = aim weapon at cursor and fire
RMB = set direction