Steps:
1. Goto http://confluence.atlassian.com/display/JIRA/Installing+JIRA+on+IBM+Websphere+6.x
2. The document is currently missing some important steps require for setting JIRA on Websphere 6.1

Points:
1. User need to delete /env/ from transaction factory in entity engine as its there in weblogic doc.
2. Websphere class loader setting. Please refer to attached screenshot.
3. User also need to increase the memory of application server, otherwise JIRA will not work. Jed can tell what should be the approx figure. I put the min 256 and max 1024 and JIRA works without any issue.
4. Can we also swap the step 2.2 and 2.3 as entity engine.xml and jira properties files are in same directory.