I bought a new chain and cassette for my drive train (triple crank, tiagra FD, 105 RD, 12-25 tiagra cassette) and the chain my LBS sold me is too long (116 links, the original chain is 114 links). I feel like I should just be able to remove the two surplus links and be good to go, but my cautious side also feels like they make chains with 114 and 116 links for a good reason. In short: get a different chain or take out two links? What would you do?

Remove two links Done!

Assuming you have a chain tool, just take out the two links.

Or, even better: check out the instructions on how to determine proper chain length, then see how much to remove.

Most chains are a standard length. Longer tandem/recumbent length chains are also available. I recently bought a longer (11' 10") chain for one of my bikes and had to remove 9". Same online retailer also sells 14" chains.

Links removed. Tension good. Thanks guys.

If the 116 fits on your bike, then tehre's no reason to cut it down. The derailleur should be able to handle the slack in the small/small combo; if it doesn't, and something rubs, then links need ot be removed, but otherwise it's actually a little bit beneficial to have extra links since the load is spread across more links.

The only thing to be cautious about is how you assembled the chain. Newer multi-speed chains (since Hyperglide) cannot simply be cut and put back together by pushing the old pin back in.

You assembled the chain with a special pin or a master link, right?

I'd like to question this statement. Seems to me that the best is to leave the least amount of links to cover the large-large gear. that way the chain will be somewhat tighter and cut down on chain bob (for lack of the better term) when going over bumps. Otherwise the chain will be looser and chances of it hitting the underside of the chainstay will be increased. No?

The parktools website has 3 different methods of determining correct chainlength. They all give roughly the same result so there is no excuse for guessing.

Regarding chain length - I size my chain for the largest cassette I plan to use on the bike. My road bike has two wheels: one with a 12-23 and one with an 11-30 cassette. The chain is sized to the 30T because if I cut it to fit the 23, it would be much too short with the 30. It's a very bad idea to run a chain that's too short, but it's not a big deal if the chain is a little too long. If it's excessively long it will rub in the small-small combo (which should never be used anyway) and as Plimogz said it can slap the chainstay.