I found myself writing many reports with LaTex lately. Using pdflatex has it advantages, but things can get quite annoying when one wants to insert a figure which was generated in Matlab or any other program.
Specially, MATLab does not do a nice job when exporting PDFs and leaves a whole blank area (the page itself actually) which is not desirable if we want to put a figure in a latex document. Fortunately, there is a linux program called pdfcrop that does the job correctly (not 100% trustable, but 90% of the times I get good results).
Another useful program is pdfimages, which extracts images from a pdf file. The pdfimages output is generally in huge pgm files, so it's better to convert it to something like png which results in smaller files, still usable with pdflatex.
Finally, pdfjoin and pdf90 allows one to join several files into a single one and rotate pages respectively. The Ubuntu package for these two is called pdfjam.