I have a 2008 imac running OSX 10.6.8. When I do a repair permissions on Disk utility I get this message: "Warning: SUID file "System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAgent" has been modified and will not be repaired. "

As long as the report ends up with 'Permissions repair complete' then, as far as permissions go, you are fine. You can ignore the various statements in the report:

Permissions you can ignore on 10.5 onwards:

http://support.apple.com/kb/TS1448

Using 'should be -rw-r--r-- , they are lrw-r--r--' as an example, you will see the that the permissions are not changed, but the | indicates a different location. This is because an update to Leopard onwards changed the location of a number of system components.

Poster rccharles has provided this description of what it all means:

drwxrwxrwx

d = directory

r = read

w = write

x = executeable program

drwxrwxrwx

| | |

| | all other users not in first two types

| |

| group

|

owner

a little more info

Before the user had read & write. A member of the group had read.

After, only the user had read & write.