First, I have also tried Goodreader. I only paid $.99 for it, but was not satisfied, mainly because it was rather hard to use and certainly extremely ugly and un-iPad-like. After looking around for a while, I settled on PDF Expert by Readdle (currently $9.99) and am very satisfied with my purchase. It can store any type of file in a very easy-to-use file system, opens images, movies, and text files, and has a great two-way Dropbox sync. Also, if you enable the built-in file sharing on your Mac, you can view and download every file in your Mac's home folder. The main point of it, however, is as a PDF Reader. Annotation, text boxes, signatures, and even are perfectly done and feel natural.
And no, I don't have any affiliation with Readdle either. I just love their app. 😉
For what you're trying to do, it's quite simple (this is if, as I'm thinking, you have an iPad with a stylus (I would recommend the Pogo Sketch if you don't have one) and you will give it to clients for them to sign). Either use iTunes File Sharing, Dropbox, or email to get the files into PDF Expert. Then open the file and tap the signature icon in the toolbar (in-between the pencil icon and the 'A' icon). It opens up a whole new pane for your client to sign in- they can even select how thick and what color they want the signature in. Tap Save. Then, in the space where you want the signature to appear, tap and hold until a selection menu appears. Tap 'Signature' and it appears, ready for you to drag into the exact place you want it. 🙂
Then, just tap the export icon and 'email', and send it away. Practically any good PDF reader will be able to see the signature. (including Adobe Reader and Apple Preview)
Hope that helps! It's completely worth the $9.99.
Liam