First, keep in mind that cat5 type of cables were designed for many uses, not only for "ethernet over twisted pair", although it's the most popular application of those cables nowadays. As you can read on Wikipedia page about "Category 5 cable" in "Applications" section:
Cat 5 is also used to carry other signals such as telephony and video
But let's get back to ethernet. If you will use gigabit connection, then all 4 pairs will be used, as you can see in this article How Gigabit Ethernet Works. With fast ethernet connections only 2 pairs are being used, as you mentioned.
So one reason to put 4 pairs in cat5 cables is that they may wanted to future proof for gigabit ethernet, so introducing in the future something better than fast ethernet will not require you to change cables, and therefore the transistion to next generation ethernet will be easier.
The additional pairs in fast ethernet networks may also be used for PoE (Power over Ethernet), as you can read here:
Power over Ethernet or PoE describes any of several standardized or ad-hoc systems which pass electric power along with data on twisted pair Ethernet cabling. This allows a single cable to provide both data connection and electric power to devices such as wireless access points and IP cameras.
That said, sometimes people who run small fast ethernet networks are using additional pairs to use them as "second cable". You just need to split cable into two on both ends (two pairs with ethernet connector, and other two pairs with other ethernet connector), and you have two fast ethernet connections using one cat 5 cable. You could actually buy a device like "cat 5 cable splitter", that will allow you to do that easily. Because sometimes it's easier to split cable, than to introduce second cable when first one is for example well hidden in the floor, or wall.
It makes sense, since you could also read on wikipedia about "Category 5 cable" in "Shared cable" section, that:
In some cases, multiple signals can be carried on a single cable
//EDIT: I found that similar question has been asked in the past on serverfault, and you could find interesting answers there to: Why do ethernet cables have 8 wires?
People are claiming there that additional pairs may also work as additional shielding. Also someone posted there example of "shared cable" use, by mentioning that you could route telephone signal in regular cable and it will work without a splitter