Q: My mac pro restarts when waking from sleep

Are you sure you installed Security Update 2013-003 (Snow Leopard)? I would recommend doing this:

Repair the Hard Drive and Permissions

Boot from your Snow Leopard Installer disc. After the installer loads select your language and click on the Continue button. When the menu bar appears select Disk Utility from the Utilities menu. After DU loads select your hard drive entry (mfgr.'s ID and drive size) from the the left side list.  In the DU status area you will see an entry for the S.M.A.R.T. status of the hard drive.  If it does not say "Verified" then the hard drive is failing or failed. (SMART status is not reported on external Firewire or USB drives.) If the drive is "Verified" then select your OS X volume from the list on the left (sub-entry below the drive entry,) click on the First Aid tab, then click on the Repair Disk button. If DU reports any errors that have been fixed, then re-run Repair Disk until no errors are reported. If no errors are reported click on the Repair Permissions button. Wait until the operation completes, then quit DU and return to the installer.

If DU reports errors it cannot fix, then you will need Disk Warrior and/or Tech Tool Pro to repair the drive. If you don't have either of them or if neither of them can fix the drive, then you will need to reformat the drive and reinstall OS X.

Upon completion reinstall the Security update using the above link to re-download. Note that if this does not work then you will need to reinstall Snow Leopard.

You can give this a try:

Reinstalling Lion/Mountain Lion Without Erasing the Drive

Boot to the Recovery HD: Restart the computer and after the chime press and hold down the COMMAND and R keys until the menu screen appears. Alternatively, restart the computer and after the chime press and hold down the OPTION key until the boot manager screen appears. Select the Recovery HD and click on the downward pointing arrow button.

Repair the Hard Drive and Permissions: Upon startup select Disk Utility from the main menu. Repair the Hard Drive and Permissions as follows.

When the recovery menu appears select Disk Utility. After DU loads select your hard drive entry (mfgr.'s ID and drive size) from the the left side list.  In the DU status area you will see an entry for the S.M.A.R.T. status of the hard drive.  If it does not say "Verified" then the hard drive is failing or failed. (SMART status is not reported on external Firewire or USB drives.) If the drive is "Verified" then select your OS X volume from the list on the left (sub-entry below the drive entry,) click on the First Aid tab, then click on the Repair Disk button. If DU reports any errors that have been fixed, then re-run Repair Disk until no errors are reported. If no errors are reported click on the Repair Permissions button. Wait until the operation completes, then quit DU and return to the main menu.

Reinstall Lion/Mountain Lion: Select Reinstall Lion/Mountain Lion and click on the Continue button.

Note: You will need an active Internet connection. I suggest using Ethernet if possible because it is three times faster than wireless.

One suggestion is to always have cloned your system ahead of time, that means before making changes or updates, early on when it is fresh and working.

And don't just restart. Use Safe Mode at least, better yet use Recovery Mode if on Lion (which I do recommend) and have a small OS Emergency drive for any maintenance - along with a clone working copy of your system.

Don't just reinstall over your system. Do a fresh install on another drive. Image it and set that for maintenance, then clone that to be a new working base for your system.

Setup Assistant does an amazing job.

Forced restarts can corrupt the filesystem and directory as the changes in memory or cache are not written out and drives are not unmounted properly and will come to bite in the rear.

Using Cloning as a Backup Strategy

Create an OS X Lion Install disc

Migration Assistant Update for Mac OS X Snow Leopard

http://www.apple.com/support/lion/installrecovery/

http://reviews.cnet.com/8301-13727_7-20080989-263/how-to-create-an-os-x-lion-ins tallation-disc

http://www.coolestguyplanettech.com/how-to-make-a-bootable-osx-10-8-mountain-lio n-disc-or-drive-from-the-downloaded-mountain-lion-app/

How to clone your system:

http://macperformanceguide.com/Mac-HowToClone-backup.html

http://macperformanceguide.com/Mac-HowToClone.html

http://www.macupdate.com/app/mac/7032/carbon-copy-cloner

http://www.macperformanceguide.com/blog/2012/20120711_2-MacPro-internal-clone-ba ckup.html

General purpose Mac troubleshooting guide:

Mac OS X: Starting up in Safe Mode - http://docs.info.apple.com/article.html?artnum=107393

What is Safe Boot, Safe Mode? (Mac OS X) - http://support.apple.com/kb/HT1564

Isolating issues in Mac OS X

Creating a temporary user to isolate user-specific problems:

Isolating an issue by using another user account

Identifying resource hogs and other tips:

Using Activity Monitor to read System Memory and determine how much RAM is being used

Starting the computer in "safe mode":

Mac OS X: What is Safe Boot, Safe Mode?

To identify potential hardware problems:

Apple Hardware Test

General Mac maintenance:

Tips to keep your Mac in top form

It will not erase your files. Note the title: Reinstalling Lion/Mountain Lion Without Erasing the Drive

so pick up Carbon Copy Cloner.

Have a drive freshly formatted even zero out.

Make a new system.

The 2008 shipped with 'bug' in EFI and SMC so that they were all doing a freeze or restart when waking from sleep. Apple issued firmware updates but always better when it ships with new chips and firmware instead.

Some 2008s had trouble with Mountain Lion unless they were careful, as in start from scratch rather than over the old system. Over time you update and update from 10.5 on and you do end up carrying a lot of old out of date drivers and such. If you have done a fresh install don't know why.

A fresh install with backup is not as daunting. Of ocurse practice makes perfect too.

Basically just format, clone, do a fresh install, and then ... carefully .... install and import files, and install a few.

http://www.roaringapps.com has a list of all the latest and what is not compatible with Lion and above.