There could be many reasons for that - did you take a note of time and impacted app ids and checked server logs? If you have any intra-day reloads this could be impacting server performance. To determine what exactly is wrong I would start from checking the events logs and confirming the size of your server (simply to reassure it's big enough to handle all of your apps, concurrent users, data reloads etc). If this issue occurred for the first time 6 months ago it would be good to review any changes that were made to your environment around that time (new apps published? in memory caching issue? new users? new jobs running on your host?).
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After messing around with this issue, I ran the Windows Memory Diagnostic on my desktop and it notified me there was an issue with my Ram. After leaving it alone for awhile, the problem came and went. When it came back in full force, I swapped out the memory from another machine and that resolved my issues. It hasn't been a long term test, but so far so good!