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I found this script which you can modify to attach a signature to an existing PDF file.

• http://emmanuel.branlard.free.fr/work/linux/dev/SignPDF/SignPDF

You can also download it from this pastebin URL:

• http://pastebin.com/9TL5pvBA

There is also this Q&A on AskUbuntu that has many other methods for doing this. The Q&A is titled: How to put a picture on an existing pdf file?.

It's worth mentioning Xournal which has a nice UI and allows adding text, images, and hand-written notes to PDF files. The only problem I've had is it doesn't seem to handle text from native PDF forms very well.

I've had a reasonably good experience with uPdf.

Installation

sudo add-apt-repository ppa:atareao/updf
sudo apt-get update
sudo apt-get install -y updf

Then fix a bug by editing 2 lines in a Python script.

Usage

Launch uPdf, select the Add an image tool, draw a rectangle around the area where you want the signature to go and select the image file with your signature. A PNG with a transparent background works best.

A lot of people recommend Xournal, but i found it to work as a version of Gimp that i can't use. Thus if you are familiar with Gimp, i would recommend trying it.

• You should have a file with the signature (even a picture taken with the phone or webcam), and a file with the document to be signed. The latter is going to be in PDF format, that can be opened by Gimp


• Apply a threshold on the signature if the white is not white enough


• Convert white to alpha in the signature if the background of the document is not white


• Open the document with Gimp


• Open the signature on top of the document as a new layer (File -> Open as layer)


• Adjust size and position


• Merge layers


• Export as PDF

I do this regularly when i need to sign single page documents, and it takes me more or less five minutes. Unfortunately this won't work if you need for example to sign every page of a multi page document. In the latter case i just print, sign, and scan again!

While putting my own signature commands into a shell script, I was looking for a way to interactively select the area where the signature should go. Luckily I found this question and the script of Emmanuel Branlard contains the idea on how to do it (with xv). I implemented the following points:

• use ImageMagicks display instead of xv
  


• use stdbuf -oL and the -update option to have a live preview


• overlay the signature with pdftk stamp to prevent image quality degradation


• only extract the specific page from the pdf file


• decrypt the signature with gpg
  


• encrypt the signed pdf file with pdftk
  


• cleanup intermediate files containing the signature with wipe
  

So here is the code:

#!/bin/env zsh

#dependencies: pdftk, ImageMagick, gpg, wipe, openssl

signature=~/PGP/signature.png.gpg

f=$1%.pdf
page=$2
density=144
bo=0.2 #baseline overlap in relation to y-size of the signature

pagecount=$(pdftk $f.pdf dump_data | grep NumberOfPages | sed "s/.*: //")
#sign on last page by default
if [ -z "$page" ]; then page=$pagecount; fi

function cleanup

 echo "Cleaning up..."
 rm $f.$page.pdf
 wipe $f.$page.signature.pdf $f.$page.signed.pdf $f.signed.pdf signature.png

trap cleanup EXIT

echo "Signing document $f.pdf on page $page."

echo "Decrypting signature..."
gpg -d $signature > signature.png
identity=$(identify -format "%w,%h,%x,%y" signature.png)
sdata=($(s/,/)identity)

echo "Please give the signature area with two clicks and finish by pressing ‘q’!"

#extract page
pdftk $f.pdf cat $page output $f.$page.pdf
cp $f.$page.pdf $f.$page.signed.pdf
size=$(identify -format "%wx%h" $f.$page.pdf)

#select signature area
display -density $sdata[3]x$sdata[4] -immutable -alpha off -update 1 -debug X11 -log "%e" -title "sign $f.pdf#$page" $f.$page.signed.pdf 2>&1 >/dev/null | 
 grep --line-buffered "Button Press" | 
 stdbuf -oL sed -r "s/^.*+([0-9]+)+([0-9]+).*$/1,2/" | 
 while read line
do
 p1=($p2)
 p2=($(s/,/)line)

 if [ -n "$p1" ]
 then
 p=(0 0)
 if (( p1[1] < p2[1] )); then dx=$((p2[1]-p1[1])); p[1]=$p1[1]; else dx=$((p1[1]-p2[1])); p[1]=$p2[1]; fi
 if (( p1[2] < p2[2] )); then dy=$((p2[2]-p1[2])); p[2]=$p1[2]; else dy=$((p1[2]-p2[2])); p[2]=$p2[2]; fi
 dy=$((dy*(1+bo)))

 if (( $dx*$sdata[2] > $sdata[1]*$dy ))
 then
 resize=$(((dy+0.0)/sdata[2]))
 p[1]=$((p[1]+(dx-resize*sdata[1])/2))
 else
 resize=$(((dx+0.0)/sdata[1]))
 p[2]=$((p[2]+(dy-resize*sdata[2])/2))
 fi

 echo "Inserting signature..."
 convert -density $density -size $size xc:transparent ( signature.png -resize $((resize*100))% ) -geometry +$p[1]+$p[2] -composite $f.$page.signature.pdf
 pdftk $f.$page.pdf stamp $f.$page.signature.pdf output $f.$page.signed.pdf

 unset p1 p2
 fi
done

if [ -z "$p" ]
then
 echo "You have to click two times. Aborting..."
 exit 1
fi

echo "Joining PDF pages..."
sew=( pdftk A=$f.pdf B=$f.$page.signed.pdf cat )
if (( page > 1 )); then
 sew+=A1-$((page-1))
fi
sew+=B
if (( page < pagecount )); then
 sew+=A$((page+1))-end
fi
sew+=( output $f.signed.pdf )
$sew

echo "Encrypting PDF file..."
pdftk $f.signed.pdf output $f.signenc.pdf user_pw PROMPT owner_pw $(openssl rand -base64 32) allow AllFeatures

(Would have left as a comment to the updf answer, but stackexchange's policy on "karma" prevents me commenting, but does not prevent me leaving an answer).

updf is really good for this. Having used preview on MacOS to "sign" documents, updf offers the closest user experience to this.

The following works on Ubuntu 14.10 and Debian 8.

I didn't want to add a third party ppa to my system, so got updf running in the following way instead:

$ bzr branch lp:updf

then made the 2 line edit as referenced from the other answer.

Install dependencies:

# apt-get install python-poppler gir1.2-gtk-3.0 gir1.2-gdkpixbuf-2.0 gir1.2-poppler-0.18 python-cairo librsvg2-2 gir1.2-rsvg-2.0 python-gi-cairo

(the above was sufficient; not every package may be necessary, though).

and then the python program is runnable in-place:

$ ./src/updf.py

Unfortunately, quality can be severely affected in the output document compared to the input document. The right way to do this would be to overlay the signature, and not change the original, in a lossless process. Whereas updf appears to engage in re-encoding of the original.

For completeness, there is an alternative script to do this, which does not convert the pdf to a (low quality) image, in contrast to the one mentioned so far: https://github.com/martinruenz/signpdf

My experience with the other solutions was:

• 
  Xournal messed with the pdf (it seemed to work after building from source though)


• The script SignPDF converts pdfs to images and reduces quality significantly. It also has a troublesome dependency (xv)


• I didn't try the gimp and updf option


• In the end I used Acrobat Reader in a VM as I also had to fill various forms

Okular PDF viewer has this built-in with annotations.
Open the PDF you want to sign, select reviews on the bar to the left, select the third option on the pop up menu that says, 'freehand line.' Draw out your signature. If you want it black ink rather then neon green, select 'Settings' from the menu, select 'Configure Okular,' select 'Annotations' button on the left. Select 'Freehand Line' from the options, then select the 'Edit' button. You can adjust both the line thickness and color here. Hit Apply and enjoy.