Before I start with the list of lists, I want to mention two apps that should not be missed:
Goodreader: Opens any document, and allows PDF annotation. It also has a handy desktop application, so you won't need iTunes to transfer files to the Goodreader.
Dropbox: Free online storage up to 2GB, very handy for transferring files to your iPad.
Here is the list of lists:
The first, and for chemists most important, list can be found on the Macs in Chemistry website. This website provides the most comprehensive list by far on chemistry related iPad & iPhone applications. Check it out!
Apple has it's own list of education oriented apps, quite a lot to search through!
A good list of reading & writing apps was posted by Online Colleges.
A nice dutch/english list which divides apps into a number of subjects.
The 'scheikundejongens' are also keen on the iPad, and made small list.
Of course, there are many more list beyond these that were useful to me. I might add a couple more lists soon, please don't hesitate to contact me for tips! And of course google can help.
Finally, I should mention the beautiful book/app 'The Elements', obviously very appealing to chemists.