When it comes to remodeling, the adage "measure twice, cut once" should always be observed. However, sometimes a piece turns out to be too small or too big. Look to see where else that piece could be used before giving up on it. If that piece cannot be cut to fit in another location, it is still usable--but it will take a little ingenuity.
Speak to the Contractor
If you are going through a contractor or have ordered the pieces from a hardware store or online service, contact them and see what they will do. They are more likely to need a piece of laminate cut to a similar length than you are, as you only have one kitchen while a contractor or store has dozens of clients. If you are paying people to cut and install them, it is their responsibility to do quality work. To avoid this before ordering always make your measurements larger than they need to be. It is much easier to trim something to fit than add something which has already been cut off.
Fill the Gap
This is the simplest, but perhaps the least attractive option available. After examining the way the countertop fits, is it possible to cut a strip of laminate or another material that fills the gap? Provided the counter doesn't have a cut-out for a sink or something else fixed, you can place the cut-out on whichever side it seems less obvious. Finally, glue the two together during installation.
To cover it finally, try and locate a putty that can cover the division smoothly and match the surrounding counter. Make sure that this is flat and level. To help keep the seam clean, cover it with a cutting board or something when in use.
Split the Difference
Depending on how large the gap is and any cutouts for sinks, mount the counter surface in the middle of the gap and fill either side with a complementary-colored piece of laminate or another material, such as finished wood. This will give the counter a framed appearance. For larger gaps, you could also split the counter in the middle as well, to give the appearance of two or three distinct work stations.
On the Chopping Block
For a considerably larger gap, this could be an excellent excuse to put a cutting surface in your kitchen. If you can find some solid wood to make a chopping block out of, you can install it instead of laminate across the top of the cabinets. If you do install a butcher's block, be sure it has an appropriate coating to withstand being used as a cutting board. Many chopping blocks also expand and contract with the humidity and weather, so be sure to install it with that expansion in mind.