Crucible/fisheye - slow. I mean really slow. Unusably slow both with respect to the UI and back end. Half our team use IE which it just doesn't work in at all. Chrome is the only thing it just about crawls along in. Incredibly difficult keeping it alive with 50 users. Crashes once a week entirely and sometimes refuses to start with no error messages at all.
JIRA - workflow crash took our team of 30 devs at the time out entirely for 2 days. Overcomplicated administrative mess especially with respect to plugins. Reindexing takes out the entire JIRA instance until complete. Permission schemes and workflow is an epic mess of cludges.
Both products: Null pointer exceptions galore, scary memory ceiling. Integration sucks - all the horrible mappings to maintain.
They feel like bloated, slow and badly designed products which is worrying considering the cost.
TBH their support are good but I shouldn't have to use it on a product suite that costs that much.