How to Clean and Store Lenses
Firstly - don't obsess over your lens' cleanliness. Many professional photographers have filthy lenses because they work their gear so hard. You really have to mess with a lens before you'll notice a difference to your image. If you do notice something, it's much more likely to be gunge on your sensor than a problem with your lens. So clean your sensor first before you touch your glass. The more you clean your lens, the more you are likely to mark or scratch the coatings on the glass which are there primarily to minimise reflections so light will more easily pass though each element. Coatings are much easier to scratch than the actual glass, and once you've damaged one it's irreparable. They are however very durable and applied in a vacuum in the factory by processes with some of my favourite names: Hard Ion Beam Sputter and Advanced Plasma Reactive Sputtering.
The reason lenses don't need to be spotless (and few are) is because they behave in the same way as your eye: when you're standing behind a chain fence and focusing through it to something distant on the other side, the chain disappears or becomes so blurry it's inconsequential.
If you're like me and you just have to keep your lens clean, DO NOT use any products marketed as lens cleaner or lens tissue paper. All you need is distilled water and cotton buds.
Blow off any dust first so you're not working it around the lens as you clean and possibly scratching it. I was told once never to blow on a lens as the acids in your breath can even damage the coating. I doubt this is true but I use canned air anyway. Otherwise buy a rubber lens blower. Dip your cotton bud in the water, roll the excess on to a tissue and work the tip in small concentric circles on the lens element. Don't apply too much pressure and regularly refresh the cotton bud. Once you've lifted any grime, a dry bud worked the same way will polish the surface. Repeat on the rear element - this will help keep your sensor clean too.
Leave a quality UV or neutral filter on your lens if you want to (I try and avoid it especially with wide angles as they can increase flare when shooting into a light source) and keep that clean and you'll never have to worry about cleaning your lens again. Hoya's new range of multi-coated filters are practically indestructible, and employ oil, smudge and anti-static coatings and greatly reduce flare and ghosting compared to cheap filters which simply aren't worth buying. Hoya makes brilliant glass and has even produced specialty glass for Nikon, Canon and Leica. Don't skimp on filters. B+W from Germany and any genuine Nikon, Canon, etc, filters are good too.
There's a lot of scary stories about mould on lenses and finding it certainly isn't joyful but once again, it's highly unlikely to affect your image unless it's severe. And it's more likely to be an issue if on the rear element than on the front. A lot of people are put off buying second-hand lenses when they find out they have signs of fungus. Consequently you can pick up insanely good deals on terrific glass on Trademe and Ebay.
The best way to keep fungus at bay is to use your gear regularly. Exposure to UV light inhibits mould growth, so if you aren't using your lenses outdoors often, leave them uncapped on a sunny window sill for an afternoon so the glass is exposed to plenty of light. And if they do have UV filters on them, take them off, otherwise this won't work. Once you do have fungus in your lens, be aware that storing it with other gear runs the risk of spreading the spores. So consider isolating any infected lens when storing. I use clear Sistema containers for storing my uncapped lenses so plenty of light is circulating around the glass and bags of silica desiccant which you can dry out in the sun. Don't buy the cheap paper ones: the glue bonding the edge fails when you dry it out and the silica leaks. ALWAYS keep camera cases stored this way away from children. Silica can look like tempting bags of sherbet. I've heard that some people make their own desiccant bags from bulk silica, or even rice, bound with coffee filters. I figure rice might eventually get dusty however.
On dust: even brand new lenses have dust inside them. Check out a lens next time you're in a store. Dust is irrelevant. You'd have to have a severely weathered lens to have an issue with dust affecting your picture. Auto-focusing, zooming and simply handling attracts dust to a lens' innards, there's just no escaping it. Let it go...