This will probably turn into a Ford vs. Chevy argument. In my opinion either one can be tuned to run and perform well. I think it's more about which are you more familiar with, which one is your IT department more comfortable supporting, and do you already own licensing for either vendor? One thing to keep in mind from a Windchill perspective, PTC provides a tool to migrate from Oracle to SQL Server. They do not provide any tool to go the other direction.
In my previous job, we did an extensive research on this during the design of a Global Windchill System to support around ~8K user base.
Here is the summary of what we found
Another consideration on your database vendor of choice should be the risk of receiving an "unfavourable" Oracle licensing audit. We have just recently had the "benefit" of a compliance audit (of our circa £50K estate of Oracle) and we were presented with a bill of £300K to pay within 30 days or face sanction !!!
It took us about a 4 man weeks of work (and numerous conference calls) to gather enough evidence to get them to accept that we were working within the terms of the OLSA and for them to finally withdraw the claim. I was worried at one point that my company was going to roll over and have to pay the bill, but we managed to fend them off eventually.
Needless to say, I have successfully migrated my TEST Windchill System to MS SQL Server and our PROD System will be switched in the coming month or so - the performance looks like it will not be impacted. This, along with re-archtecting my remote DR System to use Veeam Replication rather than Application level replication means that I will have totally eradicated Oracle from the company by the summer.
There is no way that I will ever be a customer of Oracle again.