IN_MOUSE -1

Captures the position the Windows cursor and passes that info to the game to change the camera angle. Once that is done for a frame, the cursor is returned to the center of the screen. There is nothing else applied to the data until it gets to the sensitivity, acceleration, m_yaw, and m_pitch part of the code.
Pros:

* As responsive as you can get
* It's accurate

Cons:

* The cursor can clip the edge of the window and not be able to go further, resulting in negative acceleration. The higher your Q3 resolution and framerate, the less you will run into this problem (800x600 is pretty much safe for any sens, 640x480 might have some clipping with low sens). Higher mouse sampling rates or r_finish should also be used to prevent Q3 from getting 2 or more large mouse samples in one frame.
* Must use CPL mouse fix (or alternative) to eliminate Windows enabling Pointer Prescision automatically for games in WinXP.
* Some may start to miss jumps set to -1

IN_MOUSE 1

Uses DirectInput to directly acces the mouse, bypassing the windows cursor. It also applied ~12ms worth of mouse smoothing automatically before reaching the sensitivity and acceleration part of the Q3 code.
Pros:

* No negative acceleration
* Works independantly of Windows cursor settings (i.e. Sensitivity and Pointer Prescision)

Cons:

* Uncontrollable mouse smoothing which adds latency to mouse actions.
* Delay when clicking mouse (click -> wait 12ms -> shoot = bad)