Security Precautions, Local Installs, And Excessive Privileges.

I have a few questions regarding security for my laptop.
First of all, any applications, plug-ins, etc., which are in the root level "Library" or "Applications" folder are allowed to run with admin privileges by default. There is absolutely no reason why this should be the case. Apparently, Apple decided to throw caution to the wind and assume no one would ever target a Mac for malicious purposes. How can I revoke admin status for these applications without moving them to another folder, where they wouldn't be easily accessible to every user account on the machine?
Secondly, the Installer program built into OSX is only capable of a "standard" install for every user and always demands root privileges before installing anything. How do I configure it to install only for the one user account it's running in, and without receiving admin or root privileges? If I get a program that's not drag and drop, I'm stuck manually ripping open installer packages and trying to extract the various components myself, which can be a bit of a pain. I would think there'd be some way of installing software that comes in an installer package without giving it root access; neglecting this feature creates a security hole of ridiculous proportions.
Thirdly, I'm not sure how many people have heard of Wowd, but it's a locally-installed facebook "app" of decidedly dubious origin, possibly involving an active trojan. Obviously, it came in an installer package. The Installer program, naturally, asked for an admin password to give Wowd root privileges. Installer wouldn't perform a local install without giving it root access, and the Wowd installer package was missing its "show package contents" item in the right-click menu. I was able to crack open the installer package with a program called Pacifist, and extract just the program; there was nothing else in the installer package, which seemed like it was just a ruse to convince people to give it root access by running through the Installer. Once the program was extracted and installed on a privilege-restricted account with nothing valuable on it, and deprived of admin access, I figured it was relatively safe-ish to run. Upon running, Wowd opened Safari; specifically, a Safari window pointed at http://localhost:8101/wowd/?tray on my local machine. While Firefox was sitting on the desktop of the restricted account, Safari was still sitting in the root level applications folder, which allowed it to run with admin privileges due to the bug described in point #1 above.
So, can any OSXperts here tell me whether Wowd was able to escalate itself to admin status through Safari and do who knows what to my machine? (Please do not inquire as to why I was playing with a live trojan.)
And can anyone tell me how to restrict admin privileges to the applications that really need them? The kind folks at the Genius Bar didn't have a clue how to accomplish this task, and were having trouble figuring out why I even wanted to.

First of all, any applications, plug-ins, etc., which are in the root level "Library" or
"Applications" folder are allowed to run with admin privileges by default
I'm not sure why you think so. Are you referring to the permissions on the /Applications folder itself, which are:
system - Read and Write
admin - Read and Write
everyone - Read only
These permissions mean only that an admin user can write to the /Applications folder (i.e. can save a file there), and that all users can read from the /Applications folder (i.e. can run apps from there). Those permissions don't say anything about the privileges that an application has when it is running.
Applications generally don't run with privileges of their own; they run with the privileges of the user account that is running them. For example, the permissions on the main /Library folder (HD>Library) are
system - Read and Write
admin - Read and Write
everyone - Read only
Now suppose you are running TextEdit from the main /Applications folder, and you create a textile and try to save it to /Library. Whether you can do it or not depends on the user account you are running from. Since members of the admin group can Read and Write to /Library, an admin user running TextEdit will be able to save a file there. A standard user, however, has only Read privileges to /Library, and so a standard user running TextEdit will not be allowed to save a file there. This is exactly as it should be. The write-permissions of the /Applications folder are irrelevant in this regard.

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    SEVERE: oracle.sysman.top.agent:Securing of agent step will be skipped because of the following reasons:
    1. Agent Registration Password was not passed.
    2. b_secureAgent was passed as false
    3. The flag -forceConfigure was assed from agentDeploy.sh
    INFO: oracle.sysman.top.agent:Plugin File:/users/ncgf/em_agent/plugins.txt
    INFO: oracle.sysman.top.agent:Plugin Homes found.
    INFO: oracle.sysman.top.agent:Executing command :/users/ncgf/em_agent/core/12.1.0.3.0/perl/bin/perl /users/ncgf/em_agent/core/12.1.0.3.0/bin/AgentPluginDeploy.pl -oracleHome /users/ncgf/em_agent/core/12.1.0.3.0 -agentDir /users/ncgf/em_agent -pluginIdsInfoFile /users/ncgf/em_agent/plugins.txt -action configure -emStateDir /users/ncgf/em_agent/agent_inst
    INFO: oracle.sysman.top.agent:
    INFO: oracle.sysman.top.agent:
    INFO: oracle.sysman.top.agent:The Agent emStateDir location passed is /users/ncgf/em_agent/agent_inst
    INFO: oracle.sysman.top.agent: The log file is /users/ncgf/em_agent/agent_inst/install/logs/agentplugindeploy_2013_10_16_15_08_11.log
    INFO: oracle.sysman.top.agent: The temp file created to check R/W permissions in Oraclehome: /users/ncgf/em_agent/core/12.1.0.3.0 is /users/ncgf/em_agent/core/12.1.0.3.0/rwFile
    INFO: oracle.sysman.top.agent:Plugin command completed with status=0
    INFO: oracle.sysman.top.agent:Executing command :/users/ncgf/em_agent/agent_inst/bin/emctl listplugins agent -type all
    INFO: oracle.sysman.top.agent:Oracle Enterprise Manager Cloud Control 12c Release 3
    INFO: oracle.sysman.top.agent:Oracle Enterprise Manager Cloud Control 12c Release 3
    INFO: oracle.sysman.top.agent:Copyright (c) 1996, 2013 Oracle Corporation.  All rights reserved.
    INFO: oracle.sysman.top.agent:Copyright (c) 1996, 2013 Oracle Corporation.  All rights reserved.
    INFO: oracle.sysman.top.agent:---------------------------------------------------------------
    INFO: oracle.sysman.top.agent:---------------------------------------------------------------
    SEVERE: oracle.sysman.top.agent:ERROR: The Management Agent configuration failed. The plug-in configuration for the oracle.sysman.oh monitoring plug-in may have failed, or this plug-in may not be present in the Management Agent software. Ensure that the Management Agent software has the oracle.sysman.oh monitoring plug-in, if not then retry the operation. If the agent software has the oracle.sysman.oh monitoring plug-in, view the plug-in deployment log /users/ncgf/em_agent/agent_inst/install/logs to check if the plug-in configuration for the oracle.sysman.oh monitoring plug-in failed.
    SEVERE: oracle.sysman.top.agent:Agent configuration has failed
    INFO: oracle.sysman.top.agent:AgentConfiguration:agent configuration finished with status = false
    INFO: oracle.sysman.top.agent:AgentConfiguration:agent configuration finished with status = false
    INFO: oracle.sysman.top.agent:The plug-in Agent Configuration Assistant has failed its perform method
    INFO: Cfm.save() was called
    INFO: Cfm.save(): 2 aggregate instances saved
    INFO: done waiting for Action from 15:08:10.272
    Thank you for your help AkankshaSheoranKaler. I have executed the following command based on your request. If there is any issue, please let me know. Thanks!
    "Can you run this command to make sure that the agents bits were downloaded correctly : oms home /bin /emcli verify_updates
    Share the output of the command. I am suspecting this is a know issue (Bug 17300008) but i will wait for your output.  Also if you can open an SR with oracle support to track this issue and its resolution. "
    [ncgf@nsn175-105 bin]$ ./emcli setup -url=https://nsn175-105.us.oracle.com:7803/em -u sername=SYSMAN
    Oracle Enterprise Manager 12c 3.
    Copyright (c) 1996, 2013 Oracle Corporation and/or its affiliates. All rights reserve d.
    The configuration directory "/users/ncgf" may not be local. See the "dir" option in t he help for the setup command.
    Do you want to continue using this directory? [yes/no] yes
    Enter password
    Emcli setup successful
    [ncgf@nsn175-105 bin]$ ./emcli verify_updates
    Verifying updates. Starting validation...
    Type       : Plug-in
    Description: Demo Hostsample Test Plugin
    Attributes
            Version: 1201000100
            Revision: 0
            OS Platform: Generic Platform
            Plug-in Name: Demo Host Sample Plugin
    Archives are missing from the Software Library. Unable to determine the URL for downloading the update. The update might not have come from Oracle Enterprise Manager Store.
    For each update with missing archives, emcli import_update can be used with a -force option to re-upload the archives to the Software Library.

       Hello AkankshaSheoranKaler
    We have done the following, but we aren't able to resolve this issue. Thank you for your help!
    lf
    “This  happen if the software library is not accessible, readable or unmounted (if it is in shared file system).”
    On Enterprise Manager server [nsn175-105], we did the following:
    1. we modified /etc/exports to include this line: /export *(rw,no_root_squash,sync)
    we start nfs service by executing command “service nfs start”.  
    On Management Agent server (nsn175-89), we verified that we are able to mount /export directory of EM server.
    On Management Agent server, we started firefox browser and were able to run successfully https://nsn175-105.us.oracle.com:4904/empbs/genwallet
    After making this change, we ran agent deployment again. We encountered the same error as shown above.
    “You can fix the software library or you can download the agent bits in offline mode.”
    For fixing the software library, select Setup->Provision and Patching->Offline Patching, then select Offline Patching radio button, download: https://updates.oracle.com/download/em_catalog.zip. Next upload this zip file.
    “Try downloading the bits again”
    We are not sure what agent bits are. Would you please explain this and provide procedure how we can download this?
    (Here I have attempted to fix the software library, but I am new to Enterprise Manager and not sure how to interpret this).

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