I'm making a Goliath Barbarian, the one from Races of Stone, page 150. At level 5 they get fortification as a special ability. Does it stack with the light fortification enchantment on an armor?
A related case worth handling up front just because it’s simple: if you were talking about a light fortification shield and a light fortification armor, they would not stack because they would be the same magic effect applied twice.
However, for your case, officially, the rules only ever address stacking in the case of magic effects, which your racial feature isn’t, and bonuses, which are numbers you add to a check, roll, or throw. Percent-chance effects like fortification, miss chances, and so on, are never really addressed (unless applied by a magic effect). This leaves us a few options for handling it:
The “real math” way: independent trials
Without any rule giving special instructions for handling things, you could argue that what you should do is handle it the way “real life” does, mathematically. That is, you have two separate things each saying you have a 25% chance to avoid these, that means you should roll twice against 25% and you avoid the bonus damage if either of them falls in that 25% range. The probability of at least one 25% chance coming up is \$1-(1-25\%)^2 = 43.75\%\$, for reference.
Use bonus stacking rules even though it’s not a bonus
The other obvious approach is to use the regular bonus-stacking rules. Since your racial fortification and your magic light fortification are different effects, and these are not typed, they would stack, giving you a 50% chance to avoid bonus damage.
No stacking at all, just use the highest
It’s entirely plausible, though decidedly unfun, to just say you use the highest fortification effect available.
Another way of achieving the same thing is to use the bonus stacking rules (even though this isn’t a bonus) and then treat this as a type of bonus (even though it’s not). Since they are both treated as “fortification-type” “bonuses,” they do not stack at all and you use your highest value.
Conclusion: Ask your DM
Unfortunately, the rules are ambiguous. Any of the above is a reasonable choice, so you’ll have to see which one your DM chooses.
In addition to KRyan's comprehensive answer I'd like to add that Light Fortification gives you a 25% chance of avoiding a critical hit. Getting it a second time just gives you the same ability again. A couple of examples:
An item that gives you the Cleave feat. If you already have the Cleave feat, you don't cleave twice.
An item that gives you DR (a nice adamantium breastplate for example) just gives you that much DR, if you get DR from another source (a level 7 Barbarian for example) it doesn't stack unless specifically noted. (It would be 2/- in the examples above)
Generally things with the same name don't stack in D&D 3.5e. Of course DM fiat is above such distinctions, so best to run it by your DM.