I am currently working on my first novel so forgive me for making what is probably considered the mistake of a 'novice'. My novel is set in the present, however my antagonist has a history dating back over a thousand years. When I write dialogue for him, do I write it in English and ignore the fact that he is over 1000 years old and would not have spoken English back then, or do I rewrite thousands of pages and plot points so that he speaks English... any other ideas would be appreciated!
Although I think everyone has made very valid contributions, the key thing is about whether your character is believable or not. I would find it unlikely that the reader would stop and think 'hang on...he's speaking modern English!'
Avoid very modern colloquialisms of course, but focus instead on character development, a good story and believable dialog.
If your antagonist is living in the present time (but is 1000 years old), then is there any reason to believe that his speech hasn't evolved? Think about what happens to people when they move to a new place with language patterns different from the ones they grew up with; don't they tend to adapt?
That said, people adapt slowly, and a 1000-year-old character probably has a lot of built-up habit/precedent. So perhaps he speaks a slightly different English than other characters, one infused with archaic words and odd grammatical structures. Don't go as far as Yoda, but you can make him linguistically different without having to write in a foreign language (which your readers probably won't understand).
As for the fact that he didn't speak English all that time, translation of dialogue into the reader's language is pretty common. Tolkein's elves speak Elvish but you can understand most of their dialogue -- but you still know they're not human.
That's actually a very good question.
I study Languages (Linguistics included) and, in general, people will adapt their speech faster than we tend to think. Of course, some people tend to keep their accents their whole lives (which can already be interesting for your character), but somethings will change and they will incorporate new vocabulary.
I can give you my own example: I'm Brazilian, and I'm from Rio de Janeiro state. However, I moved to São Paulo state 13 years ago. My accent hasn't changed much, I'm still identified by my accent, but it's much softer now. However, my vocabulary choice is an odd mix of words (including slang) from Rio and São Paulo - something else which identifies me as being from Rio.
However, you're talking about 1000 years and learning a different language, right? Actually, no, because languages change slowly - structurally, especially. You can still read Shakespeare, though we are about 500 years apart, but listening to the original would probably sound very strange to us. In the same way, I can read Camões, which is about 500 years old, as well, in Portuguese, with relative ease, but the Portuguese people have a harder time - because Portuguese in Portugal changed in different ways than Portuguese in Brazil did.
Take, for example, this new verb "to google". Some people won't know what it means, but most do, and depending on how the world goes on, it will be incorporated into the vocabulary canon or abandoned (check out "to defenestrate" as something that still exists but has been abandoned).
The process of learning and adapting to language changes is essentially the same: as the language changes, your character would be learning the "new language" as it changed, so, despite maybe some idiosyncrasies in speech, like outdated vocabulary or maybe a few odd words in, your character should speak English as well as the next guy.
If I understand the question correctly...
If he grew up speaking Old English (or whatever), is still alive, and communicates with present-day people, he will by definition have to have learned modern English. If he can't speak modern English (or whatever the modern form of language is), then he won't be communicating with anyone. You can allude to the fact that his language evolved over time (all living languages change as time passes).
If you don't write his dialogue in English (or whatever living language you're writing in), no one will be able to understand his dialogue. You can also have him use slightly stilted or idiosyncratic English to portray his different linguistic background.