I can't believe this is something I missed all these years. I was always under the impression that biological molecules break down very quickly upon death but apparently they have been discovering fragments (<1kb) of ancient DNA for over 30 years. Basically, they find ultra small DNA samples in fossils and inside amber (like Jurassic Park), make a whole load of copies using PCR and then analyse it. Recently they managed to extract DNA from the eggshells of the "Elephant bird" (a bit like a huge emu).
http://scienceblogs.com/notrocketscience/2010/03/dna_from_the_largest_bird_ever_sequenced_from_fossil_eggshel.php
http://www.newscientist.com/article/mg14119104.600-fact-fiction-and-fossil-dna-analysis-of-ancient-dna-should-give-clues-about-the-origin-of-species-and-how-they-evolved-over-time-but-only-if-the-dna-really-is-ancient.html?full=true
http://findarticles.com/p/articles/mi_m1200/is_n21_v146/ai_15951710/
http://www.dailymail.co.uk/sciencetech/article-1026340/Jurassic-Park-comes-true-How-scientists-bringing-dinosaurs-life-help-humble-chicken.html
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