Yes. A PCI-E card is a PCI-E card. You just want to stay away from PCI (non-express) and AGP cards.
There are different PCI-E slots, such as shorter X1, X4, and X8 slots; generally you want to avoid these as PCI-E X16 slots have the highest bandwidth and thus offer the greatest performance from your graphics card.
Here's a picture for reference. I heard that X16 devices will work fine in X8 and smaller slots, though their performance will be lessened. I haven't tried this myself, but again, from what I've heard, they will physically fit.
There are also different PCI-E versions: 1.0, 1.1, 2.0, and 2.1 (with 3.0 coming up in a year or two). Newer versions offer higher bandwidth (IIRC, PCI-E X16 1.0 is equivalent in bandwidth to PCI-E X8 2.0), but this shouldn't be a concern unless you're using some of the latest and greatest graphics cards. Newer cards are backwards compatible with older slots, and vice versa. So a PCI-E 1.0 graphics card will work fine in a PCI-E 2.0 slot.
Finally, if you're new to PCI-E or graphics cards in general, remember that there is a small tab at the end of the slot which locks your card into place. You'll need to push this tab in order to remove the graphics card when it's time.