Just enumerating some issues I have had with Winterboard (most recent version) on my Iphone- will be a bit lengthy but hopefully it will save someone time and educate a few!:

Originally the first problems (i thought) came when I tried installing SMS themes/tones via winterboard (possibly 3.X versions but some had Ios compatible in description) and it at first crashed to safe mode- which was corrected on respring.
The themes DID work but it eventually started giving me problems with BiteSMS and I no longer had any Push notifications come up when I got a message- when a message came in i would simply get the first vibrate or the tone would play.

First thought/solution- remove themes-
From Winterboard I hit select themes- deselected theme - went back and hit respring-
Crashed Again to safe mode - then respringed fine.
BiteSMS issue remained

Second solution - Reinstall BiteSMS- No fix- same issue.

Third solution - Remove winterboard -
this is when I noticed (upon rebooting) that the length of time it took to reboot significantly increased after the first issue I had with Winterboard and after almost every reboot since the first issue- it restarts in safe mode. (Hangs on the Apple logo with the spinning wheel)

Regardless of what I remove or install- since installing the first erroneous theme on Winterboard- reboot issues ensue and I am stuck with a 3-5 minute wait for the phone to restart versus 2-3 minutes. <- all of this matters when your phone crashes during a call or a text or something.

Upon learning that lesson I decided only to use Winterboard to get White Icon Labels- upon using Sauriks theme (which it comes with) I got the same issue and currently - though I've removed the themes and winterboard- I'm back to having long reboot times.
Now I dont know whats happening when it reboots but I am sure its due to the errors incurred by Winterboard allocating wrong information or whatever.

I've restored and set up as new phone Twice since i've gotten this particular phone- and upon the restore the regular speed of a 3GS returns- including some difference in battery life. (I havent watched this enough to see if its due to the winterboard issues or other things I fiddled with but I know it lasts a bit longer)

Moral of the story- Running Winterboard on IOS 4
Dont install/run previous themes on 4.0 - problems WILL ensue.
ALSO- unless it has become clear that the themes that come with Winterboard have been updated to 4.0 - DONT run those either. Phone wont be bricked or anything but it will cause an inconvenience.

Regarding compatability issues: Much more time can be saved by going here:

P.S.S.- if somethign similar has been posted-
forgive me for not having read it- frustration motivated me to write this...