Fallout 3 has the much more interesting open world in my opinion. NV's is more bland and more static; certain creatures are always roaming around in the same areas, much more than FO3. There's a lot more emptiness and nothing beats exploring the ruins of DC, and you'll find more hidden and/or unmarked side quests in FO3. It's way more dangerous too, NV has safe hubs everywhere.
On the other hand, FO:NV is better in just about every other way. It's a much better Fallout game; the tone and writing are much more like the original Fallout games. Obsidian actually attempted to create a good story with FO:NV and they certainly did; it branches out far more than FO3's (and most other RPGs), there's a lot more depth to the writing, and it creates some very memorable characters (perhaps the next best after Bioware RPGs). It has a lot more quests in general too.
Gameplay in FO:NV is better in just about every way too, from the new faction reputation system, disguise system, the built-in Hardcore mode (though mods enable this in FO3), the weapon customization, addition of iron sights, melee combat system, better use of perks.
Both of them are must-haves and are some of the very best games out there. FO3 is a lot more unstable especially with mods; I managed to get it stable with these mods
, but only on one of my computers. It's completely unplayable on the other when using those mods. It's still worth a try definitely. Mods are a necessity for both, and only play them on Very Hard difficulty.Edited by boredgunner - 11/17/13 at 12:05pm