Taken directly from their website. My guess is that your have to re-pwn your iPhone with 1.1 to get the new features.

EDIT: The custom packages is sweet. You can now add things like BSD Subsystem and OpenSSH directly to your hacked firmware. Negates the need to have to reinstall things after each restore. Would be nice to have the AUS localisation packages, as this will surely save a lot of time.
See this link for a screenshot of the custom packages screen.
iPhone Pwnage Tool updated to 1.1 with support of custom logo—winandmac.com
Link to iClarified where they will be hosting a new guide shortly
iClarified - Apple News - PwnageTool 1.1 for iPhone is Now Available!

The “DevTeam” would like to announce the release of the 1.1 version of the PwnageTool application. The application will automatically update from 1.0 to 1.1 using the inbuilt application updater.

Changes and fixes:-

EDGE settings fix for iPhone 1.1.4 firmware
iPhone/iPod firmware 2.0 5A240d support
New Features

Added custom package support
Added custom logo support
Added auto delete of BootNeuter.app
The application can be downloaded directly from http://xs1.iphwn.org/appcast/PwnageTool_1.1.zip

Certain portions of PwnageTool will be released under the GPL, the first being “iPhone Firmware Tool”. Expect to see the source code for “iPhone Firmware Tool” posted on the iphone-devteam google code page within 48 hours of this release. Further source code releases will follow in good time.

We would also like to mention that the development of a Pwnage application for Windows has taken cmw longer than originally anticipated. The windows version is not a Dev Team release. “cmw” is working on an independent tool called “winpwn”. We don't have timelines or release dates, but you can read about his progress at Main Page - WinPwn.

Anyone else tried Pwnage Tool 1.1

I used it yesterday. It was my first use of Pwnage, and I encountered a few little difficulties along the way. Judging by the guides, my phone should have still been in recovery mode after the "iPwner" stage, but it wasn't. No big problem putting it back into recovery, but a bit confusing.

The options to bundle BSD subsystem and OpenSSH didn't work. Installer was installed, but not those two. Again, no big problem. I was able to install them through Installer.

I had the IPSW Builder fail the first time, but it was okay the second time.

Then after getting it all going, iCal was playing up. Despite having set all the time zones correctly, it was adjusting all my appointments by the time difference between Melbourne and Cupertino. Tried everything I could think of, and eventually redid the restore to custom firmware, and the second time it was all right. I don't know whether that had anything to do with pwnage or not, but that's what happened.

However, despite those little glitches along the way, it is now all working perfectly.

So my review would be that iLiberty+ was easier to use, and I can't tell the difference in the final outcome. However, my limited understanding of all the technical descriptions would suggest that pwnage probably has some ongoing advantages "under the hood".

I haven't used 1.1 yet as my phone seems to be working perfectly on 1.0. I am leaving well enough alone and will only try a later version of Pwnage if I run into issues with my phone. I don't install a lot of programs so the only things I would like included in my custom firmware are BSD Subsystem, OpenSSH and the AUS localisations.
Sorry to hear you had so many problems. Hopefully they make 1.2 easier to use.

Just tried 1.1.. not really worth the time compared to 1

care to elaborate?

Well, I spent about 4.5 hours last night with a range of tools. Pwnage was one of them, and I followed the instructions to get up to the 2.0beta firmware. However, it currently does not function as a phone (damn!), and the WPA(2) Enterprise seems to only support MS-CHAP authentication, not PAP as require by eduroam (double-damn!), but the Cisco VPN client works a treat! I'm going to spend a bit more time on the weekend to try to get it fully functional again.

oh i am SO looking forward to that
(wpa enterprise)

i cant wait for my iphone to arrive

1.0 for the win

Worked fine for me bar the recovery mode issue above. For some reason I needed to add + 61 too all my mobile contacts for it to work. Other than that PWN is awesome