This is the way I run Swain, its not pro its not special, infact the only reason I wrote a guide on here is to show my friends. That being said please don't troll it, it's use is intended for my clan and friends, not to be some pro guide. OK, so getting into the actual guide.

Pros:
Devastating late game.
Tanky even without defensive items. (the more damage you do the more you heal)
Can take on half the enemy team solo if you're fed.
Slow + Snare
Rediculous DoT

Cons:
Terrible early game, one of the weakest champs until level 4, at which point it turns around.
No skill escape (hence why we bring flash)
Bad Swain is bad. Requires more skill than most people think to be halfway decent.
Dependent on blue buff to own half the enemy team.

Why these two spells? Well because I said so. If you're really wanting an answer to that then read on.

Ignite: Ok you all know what ignite does, DoT + counter heal etc, useful for many champs. Why not exchange this for something like exhaust? Because the damage increase from Torment affects Ignite, amplifying its damage even more... need I say more?

Flash: No built in escape, Never Move + Flash = Good bye. You could change this out for Ghost if you wanted, but with Swain possessing both a slow + snare I find it easiest just to slow them/snare, limp to a wall and flash through for my getaway.

Why these runes?
MPen for more damage, more damage = more heals.
Mana regen for more mana, swain is extremely mana hungry, either way you'll need blue buff to be a dominating force.
MR, MR is always helpful when you have slow + snares, melee will have a hard time getting to you, more defense against other mages is helpful here.