It's a constant battle between function and looks for me too. I ended up putting my daily coffee stuff and a few nice looking spice jars up high, but the ugly plastic containers stay hidden. The trick is to only stack things that are light and you use all the time, otherwise you'll never grab them. It forces you to really cut down on the clutter, which is good for a small space.
What kinds of things did you decide were shelf-worthy up there? I'm always torn between wanting my most-used stuff handy and not wanting the shelves to look too messy. My tiny kitchen forces some hard choices.