Openings of all kinds are found in all kinds of rocks. Here are the most important types of holes in geology (natural ones, not the holes that geologists make). Sometimes a hole qualifies for more than one name, so be careful with your observations.
1. DruseDruses are small cavities that are lined with crystals of the same minerals that are found in the host rock. "Druse" may also refer to a surface carpeted with crystals, one with a drusy texture. The word is from German.
2. GeodeGeodes are small to medium-sized cavities, typically found in limestone or shale beds. They are usually lined with at least a thin layer of chalcedony, and they often have a drusy lining of quartz or calcite crystals. More rarely, the drusy lining is other carbonate or sulfate minerals. Geodes are capable of weathering out of the rock as discrete concretions or nodules.
3. LithophysaLithophysae are found in high-silica lavas like rhyolite and obsidian: they are round hollows lined or filled with feldspar or quartz in concentric layers. It's not always clear whether to consider them bubbles or droplets (spherulites), but if they empty out they are clearly holes. The name is Latin, meaning "rock bubble"; lithophysa is the singular and lithophysae is the plural.
4. Miarolitic cavityThis is a special type of small cavity found in coarse-grained igneous rocks like granite, especially in late-stage settings such as pegmatites. Miarolitic cavities feature crystals of the same minerals as the rest of the rock (the groundmass) protruding into them. The name comes from the Italian miarolo, the local dialect name of the granite near Lago Maggiore whose crystal-lined pockets were once famous among mineral collectors.
5. MoldMolds are the openings left behind when minerals dissolve or when dead organisms decay. The material that subsequently fills a mold is a cast. Fossils are the most common kind of cast, and casts of easily dissolved minerals like halite are also known. Molds are temporary things, geologically speaking.
organic weathering. Other marine creatures make marks in rocks, too, but the real holes generally belong to pholads.