Proc alerts are simple. I use Satrina Buff Frames for my buffs and debuffs. I just make a third frame and whitelist Freezing Fog and Killing Machine. I put this buff bar right under my character. Made it click-though and semi transparent. Now I can easily see my procs without an extra addon.
As for Runes, I just use the built in rune display for Pitbull 4. My rotation is solid so my Runes rarely need a looking at. Also, it takes half a second to glance down at them, the same amount of time it would take to glance at a Rune CD addon.
So, no extra addons, just using the same ones I have for other things.
I have Magicrunes with a rune display over my character so I'm always looking @ my runes. Also my Parrot scrolling battle text has Freezing Fog and Killing Machine procs explode on my screen in big bold letters. It helps a lot cause I still am in the process of automatically hitting the HB button when it procs.
I use the addon NeedToKnow. It allows you to custom track debuffs/buffs on you/target, with whatever combo you choose. It gives you nifty little bar groups that you can scale, move anywhere, decorate, etc.
I have one bar group set for diseases, idealy. Then theres one for my buffs. I put KM, Freezing Fog, and UA together close to the center of the screen to see them.
For runes, you could get Runewatch. It looks pretty, has its own disease tracker, runes and RP all in one compact frame.
i use power auras. it tracks everything, diesases, procs like KM, Rime, SD... you can program it to pick up just about everything. it's all in one need mod.