[NiteWave]

I tried to set
LSAPI_MAX_PROCESS_TIME (default value: 300 seconds)
"In Self Managed Mode, LSAPI_MAX_PROCESS_TIME controls the maximum processing time allowed when processing a request. If a child process can not finish processing of a request in the given time period, it will be killed by the parent process. This option can help getting rid of dead or runaway child process."
it looks working in test environment.

your php in suExec mode or not? if not, above setting will give you an option.

update: I re-read your post:

I look at mytop and see 4 or 5 identical long queries running because they are from the same user and their process is just trying and retrying.

it may not result of "re-try". rather, there are 4 or 5 independent requests to same page, and this page need access mysql. for each php request, lsws has to launch a lsphp process to handle it. I think the root cause is slow mysql. if you use memcache to cache the mysql query result(just for example), mysql and the whole site's performance may improve a lot.