Some people like the quieter clicks, I am not one of those people. It started to really get on my nerves. If I want quieter clicks, I can just turn the volume down. They should have left things alone, but since they didn't I had to figure out how to get it back to the way I like it. Here's what I did. You must have a jailbroken iPhone in order for this to work... obviously.
1) SSH into the iPhone and then go to System/Library/Audio/UISounds
2) Grab the file "Tock.caf" and put it on your computer
3) Using Audacity (free) open the file and then using the Effects, amplify the sound to about twice what the original file is
4) Save the file as a .wav
5) Download ToneFXsCreator (also free) onto your computer and download ToneFXs via Cydia onto your iPhone
6) Connect iPhone to computer via USB cable
7) Open ToneFXsCreator and find the new .wav file and open it
8) Make sure "fade in" and "fade out" are unchecked before you send the tone to your iPhone
9) Send the tone to your iphone
10) Open ToneFXs on your iPhone and find in the list where it says "Keyboard Click" and select it. It should give you a list of sounds to choose from. Select the file you sent to the phone and it will give you a preview
11) Go back to the main screen of ToneFXs and then save. The phone will respring and you'll have your wonderful loud clicks back. If you want them quieter for any reason just turn the ringer down
When you select the file in ToneFXs is will give you a preview. The preview may seem WAY too loud and that loudness will make the click noise sound horrible. Don't get scared off now, you're so close. I'm not quite sure what Apple did to make the clicking quieter, but they did NOT change the actual sound file. If you were to go into Settings on the iphone and test the sound, it is loud like it was just before the 3.1 update. So while your new sound may seem WAY too loud, something somewhere in the iPhone is telling the keyboard clicks to tone it down some. So with your new audio file it will do the exact same thing. So while the preview in ToneFXs may seem horribly loud, once you save and respring and test it out, it will be just perfect.
I can't believe no one else has mentioned this here. I am hardly the authority when it comes to stuff like this and I managed to figure this out on my own with a bit of creativity. Hope you enjoy.