Pen storage seems mainly to be an issue of personal preference and experience. The proper position for an unused pen varies by the type of ink and even certain geographical considerations such as humidity and altitude.
Generally speaking, you want to keep ballpoints tip down so that the heavier, slower-moving ink is at the tip of the pen when you need it. Gels and liquid ink pens are best stored tip up or horizontal to keep pressure off the tip and prevent leaking. Inked fountain pens should be tip up to keep ink from clogging the feed.
Other than that, here are a few suggestions for getting the best out of your pens.
1. When in doubt, go horizontal. The ink will be evenly distributed in the cartridge, which should help it return to action more quickly.
2. Never leave a tip exposed. Cap stick pens and fountains, make sure to retract click pens. This helps keep air away from the ink, so it won't dry out as fast.
3. Avoid extremes. Probably not a good idea to keep your pens under a bright lamp or near any other source of heat, or to leave them in an unheated room during cold weather. That's a sure way to dry out or clog up the ink.
4. Pick your surface carefully. There is always the chance a stored pen is going to leak. If you put your pens into a container that you love, or lay them on top of important papers or a favorite fabric, there's a good chance it will end up ink-stained.
If anyone else has any tips on the best way to store pens, please chime in. We'd love to hear how you handle your collection.