Would you say 3.5 is the most popular?
Well, each to their own. Most stores only sell 4.0 now and most places that have periodic games are usually 4.0.
I, however, have been involved in 3.5 for a while and thus am reluctant to convert.
When you choose which one you want to play, there are a number of things to keep in mind. 3.5 and 4.0 are really different games. They are so different that you
cannot convert from one to the other as you could with older versions.
3.5 is a more classic version of DnD and has a lot more books, but you have to buy them at specialty stores or online. 3.5 focuses around feats and uses a level-based spell system. 3.5 also allows for a lot more customization between prestiege classes, multiclassing, a wider array of feats, etc.
4.0 is much newer and is actively being worked on. All powers and combat are based on "Powers" that all classes get. These powers are daily, encounter, or at will. They allow for more in-depth combat and interesting strategies. Unfortunately, they got rid of the old spell system and now wizard spells are just powers. In general, feats are pretty vanilla. They've eliminated multiclassing and prestiege class and instead have "Hybrid" classes that allow you to fully combine two classes and paragon classes that are branches off of your main class that you choose when you reach level 10.
I suggest you research further, though ultimately it's a matter of taste. I'm sure you can find debates online...
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