Would have also suggested Note Taker HD, however it does export sub-selection areas of a work file. Other then that it's a very hand note taker. I'm considering it for use as a student work app. So they can "write" on digitally provided worksheets.
No issues with good reader. What did you feed it? Even with 512 ram in the iPad 2 it GoodReader does have it's limits. If it keeps crashing go to the iPads Setttings and find GoodReader, click the toggle to force it to start clean. Then double check the file you think is giving you trouble.
It could also be that your iPad needs a short rest, full shut down and boot up. Used to have to do that on my iPod.