Lot of people asking this question, though i would help out.

Method 1

Put into DFU mode, robotic instructions here, lol.
On your computer... Start > Control Panel > System > Hardware > Device Manager
Find "Universal Serial Bus (USB) Controller", subitem Apple Mobile Device USB Driver.
Right click, choose Properties, go to Details, select
Device Instance Path from the dropdown box. The end of this info string will tell you the bootrom version, e.g. iBoot-359.3.2

iBoot-359.3.2 is the NEW BOOTROM
iBoot-359.3 is the OLD BOOTROM

Method 2

Install usbview link here
Put the iPhone 3GS in DFU Mode
Run the Application usbview
Check if you find:

iBoot-359.3.2 - then its the new bootrom
iBoot-359.3 - is the old one

source

DFU Mode

1. Connect your iPhone to your computer.
2. Turn iPhone off.
3. Hold power and home together for 10 seconds (exactly).
4. Release power but keep holding home until the computers beeps (observed on a PC) as a USB device is recognized.
5. A few seconds later iTunes should detect your iPhone.
6. If the Restore Logo is present on the screen, you are in Recovery Mode, not DFU

Good to see this in it's own thread. You neglected to mention how to put the phone into DFU mode

Also, very useful - the ECID can also be obtained via the same process. 3GS owners can request their SHSH via The Firmware Umbrella without even jailbreaking.