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I was able to repro on 2008 R1 SP3 10.00.5512 but installing the latest CU (14) fixed it. Reviewing the bugs fixed in the intervening versions it looks as though you need to upgrade to a build that includes the following fix. Access violation when you run a query that contains many constant values in an IN clause in SQL Server 2008 or in SQL Server 2012 ...
Follow the steps outlines in How to use the DBCC MEMORYSTATUS command to monitor memory usage on SQL Server. The remedy action will depend on your findings. You can also read How to Identify Microsoft SQL Server Memory Bottlenecks which is more accessible. One word of caution though: is unlikely you will find individual queries to blame. Tracking downs ...
I take it you are using REPAIR TABLE by hand. I also take it your are doing an automatic table repair for MyISAM. (You have to remove or comment out the option of my.cnf to disable automatic MyISAM table repair). You can actually repair the table without using MySQL but mysqld cannot be accessing it. How? You have to use the offline utility myisamchk ...
The best database will be the one you (or the person in charge) know how to administer and handle. Besides software resources, one important question is the human resources you have available for your project. Oracle, Sql Server... will all be useless if no one in your company knows how to use those DBMS.
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