You don't need to start over, unless you want to do the Vault 101 side quest if you missed it. It's an awful long game to just start it over, but if you want all the achievements (Xbox 360) then I would advise you to do so, unless you have a save file from the middle of the game, then use that one. That way you can recieve the transmission to go back to Vault 101 for that side quest.
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I started again so I could get the achievements for alignment eg. Neutral/Evil, also meant I could pick up a couple of side quests and complete DLC, Broken Steel the new DLC allows you to play up to level 30, I love RPG so starting over not too much of an issue.
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If you don't have the "Broken Steel" download then you will want to complete the side quests before the last main quest "Take it Back". But you don't need to start over to complete the side quests.
If you have the new DLC "Broken Steel" you are supposed to be able to keep playing after the end of the main quest, so you could do the side quests at your leasure. But most folks that like this game will start a new character at some point and replay most if not all of the game over. There is a lot of replay value in Fallout 3.
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