Water-based stains are the finishes most likely to raise wood grain. Unlike oil, water seeps into the cells of the wood and causes them to expand. The darker grain patterns have smaller, tighter cells, so when they expand, they naturally rise from the surface of the wood, creating a grain texture. This texture is typically unwanted, since it allows the grain to be damaged more easily and traps moisture in this raised surface.
In order to properly apply water-based stain, you should be prepared for an extra sanding step. Wet the wood with normal water before you stain. Wait for the grain to swell, then sand it down until the grain is smooth again. Wait for the wood to dry, then apply the water-based stain. This should bring out the pattern of your grain without actually caused the grain to swell.
Stains come with a number of toners and dyes that can have different effects on the wood. Wood toners are water repellents designed to highlight grains which can prevent swelling problems caused by exposure to moisture. Dyes can be used to highlight grains and penetrate wood surfaces without raising the grain as much as a water-based stain would.
When using pigmented stains, always choose a clear or semi-transparent version to best protect the wood and highlight the grain without covering it up with a thick coat of stain. You do not want to spend the time sanding down the grain and then obscure it with your finish. Avoid thick finishes like gel coats for the best-looking grain possible.