How are lens flares akin to that in shows like Battlestar Galactica, SGU, etc. achieved?
Here is an example:
I think the type of lens flare you're looking for is anamorphic lens flare.
All the main editing packages have lens flare as an option, so this is incredibly easy in post.
To do it live is less controllable, but is still simple - in fact avoiding lens flare is one of the challenges, as many lens configurations give unpleasant flare when shooting anywhere near the sun.
If you have an editing package, you can see if any of the popular lens flare plug-ins are available for it. For example:
I know that Motion has a built-in lens flare generator. I'd assume most other packages do, too.