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What are the differences, other than a file size restriction in SQL Server Compact, and Windows only usage?

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Why are you looking for an alternative? Whether SQL Server Compact Edition is a sensible alternative depends on your answer. In our case, it certainly is not a sensible alternative, but our requirements are certainly different from yours. –  Samuel Neff Jul 21 '10 at 16:49
@Sam: In a Microsoft-only shop, it is problematic to introduce open-source software that doesn't have Microsoft's blessing, especially when there is a potentially viable alternative available from Microsoft. –  Robert Harvey Jul 21 '10 at 17:08
agreed, if your requirement is "use MS whenever possible" then that changes the arguments for SQL Server Compact Edition vs SQLite. –  Samuel Neff Jul 21 '10 at 19:01
Unfortunately MS EULA's prevent publishing performance statistics without permission so you won't find many performance analysis out there, but you should do your own comparisons with your types of data so you know how big the difference is. In our situation, we were very surprised at the results. –  Samuel Neff Jul 22 '10 at 3:09
Also see stackoverflow.com/questions/2278104/… –  nawfal Feb 19 '13 at 13:28
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up vote 2 down vote accepted

I've found a couple of questions and some blog posts relating to this. A small comparison of their memory usage can be found here.

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