Read This before installing Winterboard
I'm seeing a lot of reports about people installing Winterboard, rebooting their iPhones and being stuck on the Apple logo.
Here is how you avoid that problem!
First, you need to JB your iPhone using purplera1n RC2, RC2a or redsn0w 0.8. If you did a JB using purplera1n RC1, then you MUST run the latest purplera1n on your iPhone again in order to receive additional kernel patches. Do not worry, you do not need to restore, just run the program again right over top of your old JB. If you do not know which version of purplera1n you used to JB your 3GS, then it's perfectly safe to download the latest version and run it again. The update is fast, so no worries.
Secondly, you MUST have the latest version of Mobile Substrate installed. The latest version is 0.9.2958-1. You can just load up Cydia, search on "Mobile" and you should find Mobile Substrate.
When you install Winterboard, make sure it's the newest version, which is 0.9.2958-2.
And lastly, if Cydia tells you to upgrade a component on your iPhone, do it!
DO NOT USE ICY to make this upgrades! I cannot stress this enough. While I prefer Icy over Cydia, Icy seems to lag behind Cydia when it comes to version numbers.
If you have tried installing Winterboard and are stuck at the Apple logo, then I am guessing you did not do one of the things I listed above. I'm sorry, but you likely need to put your iPhone into Recovery or DFU mode and do a restore.