The problem: (pdf)LaTeX creates loads of intermediate files before it creates the PDF file. This results in your directory being cluttered by useless files (.log, .aux, .vrb and so on). You may try to get rid of them by using the command pdflatex --output-directory=.tmp in TeXShop, but then your PDF file won't automatically show up (because it also ends up in the temporary directory). Here comes a possible solution.
Save the following python script in a location of your choice (say /Library » TeX » Root » bin » pdflatex.py):
tmp_dir = '.tmp'
import os, sys, shutil
tex_file = sys.argv[-1]
f, ext = os.path.splitext(tex_file)
assert ext[1:] == 'tex'
if not os.path.isdir(tmp_dir):
os.mkdir(tmp_dir)
os.system('pdflatex --shell-escape --output-directory=%s %s' % (tmp_dir, f))
shutil.move('%s%s%s.pdf' % (tmp_dir, os.path.sep, f), os.curdir)/usr/bin/python /Library/TeX/Root/bin/pdflatex.py
Now every time you hit the Typeset button in TeXShop, only the created PDF files will be visible in the Finder. If you want to access the intermediate files in the Finder, simply hit Shift-Command-G and type .tmp.
Mac OS X Hints
http://hints.macworld.com/article.php?story=20070906022746216