I was asking our VAR the same question, since I've received an email regarding that SEPDM 2009 SP.3.0 could randomly check files in and out of the system, and this was fixed in SEPDM 4.0
We are running SW2009 SP3.0 at this moment, and nothing major has happened, but when rolling out SEPDM2009 SP4.0 SW is upgraded as well.
So SP 4.0 in both SEPDM and SW.
As i saw on one of client end i found that in Solidworks Enterprise PDM 2009 sp 3.0 have several problem like
1- Slow workflow performence
2- For Compatibility with Solidworks you have to use a patch
3- Workflow hang or crashed when try to save any modification
4- Slow speed of check in and check out(not that much but still have some issue regarding speed)
These all the problem now resolved in Solidworks EPDM 2009 sp 4.0