Can certain bitcoins be worth more based on the transaction used?
Just like physical coins and bills have numismatic value, bitcoins from certain blocks could have numismatic value as well. This could be due to the block's low number, or because the block is special -- such as block 140,000 from a few days ago, which contained the last of the first 1/3rd of all bitcoins to be issued. Your example, of coin whose immediate parent was part of the 10K BTC pizza purchase, is another.
The problem is that because the coins are data and can be copied, transferring these coins to a new owner without creating a new transaction involves trust that the previous owner will destroy any archives and not spend the coin. This trust requirement is likely why there is no collectible market yet for bitcoins, and why there probably won't ever be much of one.
Virgin bitcoins (generated but never spent) can have value due to them having no prior history. If you have generated coins, there is no prior transaction in the blockchain that might be used to help learn your identity. Though with the current difficulty levels the ability to earn virgin bitcoin from solo mining is getting close to impossible, those in the P2Pool and Eligius mining pools do generate virgin bitcoins directly to the miner and those coins have no prior history.
While there was at one time miners selling virgin bitcoins on the #bitcoin-otc marketplace, those types of offers aren't seen very often anymore, so the conclusion might be made there really isn't much of a market for virgin bitcoin either.
That being said, I'm sure the value of the 50 BTC (plus tips that have since been received) held (presumably) by Satoshi are worth way more than what 50 X $[current market rate] would ever return.