OK, if I understand correctly, you can't make assumptions about the size of what the full regex would possibly capture. But can you at least make some assumptions about the size of the start tags and end tags? If you can do that, then reading the file by chunks is a perfectly workable solution.
You basically need 2 patterns that will match the start and the end tags (or more patterns if there can be several sorts of start and end tags). Then you implement in your code a state machine or a mini-parser that looks for the start tag; when you've found one, you capture everything that comes from the file until you reach the end tag, and start allover again if this is what you need. For managing the chunk boundaries, you just need a sliding window (as already discussed) that is as large as the maximal length of the start or end tags.
Edit: @ Nocturnus: because I spent some time reading the various comments, your last message just above was not on the page I was reading when I wrote this message (in other words, I loaded the page before you posted this last message). Therefore, my message is not an answer to your very last message, but rather to the previous ones.
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