The work pretty much the same.
But if you want to play online, you'll find that 90% of the games are 3.5, as most people cannot stand playing something earlier than the latest edition (unless it's vintage).
Furthermore, it depends if you're planning to buy many supplementary books afterwards. If you are, 3.5 is better for you since they'll be releasing more and more books in the next year, while 3.0 supplements are only those published so far.
With one caveat tho... If you want to play Forgotten Realms, I think you'd better join 3.0. The reason is the cost: FR was the #1 supported setting when 3ed came out, so there are many FR books written for 3.0. You need the FR Campaign Setting, Monsters of Faerun and Magic of Faerun, plus I'd suggest Faith & Pantheons. If you play FR in 3.5 you still need the 3.0 books because the setting information is not reprinted anywhere else, but you'll also need the 3.5 books where spells and character material is reprinted, and you'll end up spending a lot on obsolete stuff.
For example, the newest Spell Compendium is NOT a Forgotten Realms product, and yet it's the only source for many FR spells in 3.5 version. So while in 3.0 you'd just need FRCS + Magic of Faerun to play a wizard, in 3.5 you kind of need FRCS + Magic of Faerun + Player's Guide to Faerun + Spell Compendium, but you'll be using the first 2 only for flavor text and not game mechanics, and you'll be using Spell Compendium for only a bunch of Faerun spells.