I generally try to get a special edition if I can, but there's times where I've been unable to or didn't.
I was going to get the BioShock 2 special edition but I got the standard game for £20 (yay Steam), and since completing it I'm actually glad I didn't. As much as I loved BioShock 2, there's no way I can justify £40 on a 6-7hr game.
Mass Effect 2 and Dragon Age: Origins I own in Digital Deluxe forms (Sort of wish I hadn't with Mass Effect 2, glad I did with Origins so Yay Steam Sale!)
I wish I'd gotten the Age of Conan special edition (it's very nice) even though I don't play AoC, and I wanted the King's Bounty: The Legend/Oblivion/LotRO: Mines of Moria/Fallout 3/Far Cry 2 special editions. I love it when it costs the same (or ~£10 more) but you get so much more.
Also wish I'd gotten the Lawful Good edition of NWN2 instead of Chaotic Evil