You can compile plugins within ImageJ using either the

Plugins>Compile and Run command or by pressing ctrl-r

(File->Compile and Run) in ImageJ's built in text editor.

The plugins contained in Input-Output>QuickTime_Plugins.jar

(Mac OS X only) are preinstalled as the File>Import>Using QuickTime,
File>Import>Video, File>Import>QuickTime Player and
File>Save As>QuickTime Movie commands.

The following third party plugins are included with ImageJ 1.49:

Analyze Reader/Writer (Guy Williams)

File>Import>NIfTI-Analyze, File>Save As>Analyze 7.5...
http://imagej.nih.gov/ij/plugins/nifti.html

Auto Threshold and Auto Local Threshold (Gabriel Landini)

Image>Adjust>Auto Threshold..., Image>Adjust>Auto Local Threshold...
http://www.dentistry.bham.ac.uk/landinig/software/software.html

Bezier Curve Tool (Berin Martini)

Toolbar>>Bezier Curve Tool
http://imagej.nih.gov/ij/plugins/bezier-tool/

Biorad Reader
Plugins>Input-Output>Biorad Reader
http://imagej.nih.gov/ij/plugins/biorad.html

Deltavision Opener
Analyze>Input-Output>Deltavision Opener
http://imagej.nih.gov/ij/plugins/track/delta.html

DM3 Reader (Gregory Jefferis)

Analyze>Input-Output>DM3 Reader
http://imagej.nih.gov/ij/plugins/DM3_Reader.html

Exif Reader (Gali Baler)

File>Import>Exif Data
http://imagej.nih.gov/ij/plugins/exif-reader.html

Fast Filters (Michael Schmid)

Plugins>Filters>Fast Filters
http://imagejdocu.tudor.lu/doku.php?id=plugin:filter:fast_filters:start

Find JAR for Class (Johannes Schindelin)

Plugins>Tools>Find JAR for Class
plugins/tools/Find_JAR_for_Class.java

Fit Polynomial (Michael Schmid)

Plugins>Filters>Fit Polynomial
http://imagejdocu.tudor.lu/doku.php?id=plugin:filter:fit_polynomial:start

ImageJ 3D Viewer (Benjamin Schmid)

Plugins>3D>Volume Viewer
http://imagej.nih.gov/ij/plugins/3d-viewer/

Interactive 3D Surface Plot (Kai Uwe Barthel)

Plugins>3D>Interactive 3D Surface Plot
http://imagej.nih.gov/ij/plugins/surface-plot-3d.html
Kalman Stack Filter (Christopher Philip Mauer)
Plugins>Filters>Kalman Stack Filter
http://imagej.nih.gov/ij/plugins/kalman.html

LSM Reader (Patrick Pirrotte)

Plugins>Input-Output>LSM Reader
http://imagej.nih.gov/ij/plugins/lsm-reader.html

Volume Viewer (Kai Uwe Barthel)

Plugins>3D>Volume Viewer
http://imagej.nih.gov/ij/plugins/volume-viewer.html

Zeiss ZVI Reader

Plugins>Input-Output>ZVI Reader
http://imagej.nih.gov/ij/plugins/zvi-reader.html