Looking for a good tool for repeat masking in long sequences The repeat masker site has a size limit of 90kb. 
Where can I mask repeats in a 500kb sequence?

Ideally, I need a thorough repeat masking of known and de-novo found repeats of various complexity. I am working on Windows but can access Unix too.
RepeatMasker can downloaded an run locally. There's then no size limit, though do note that it's quite slow for mammalian-sized sequences (you'll want to split it into chunks and run in parallel in such cases). For a small 500kb sequence that won't pose an issue.