The way MR is calculated is:
Your magic resistance divided by your magic resistance plus 100. In numbers
MR
MR+100
Starting out most champs have about 25% reduction (your bombs were doing lets say 500 damage now they do 375 damage) this almost never increases without times. Buying a Negatron Cloak will put you at about 50% reduction (bombs now do 50% damage)
To counter:
Void Staff - This penetrates 40% of their MR Meaning that if they have 200 MR (67% reduction) you would deal 13% more damage (reduces MR by 80)
Sorcerer's Shoes/Haunting Guise: these penetrate MR by a flat amount (20) meaning that they are more useful if the enemy has low MR you will deal more damage (about 15% if they dont have any items) however if they have 200 MR you will deal only 3% more rather than the 13% with a Void Staff
Abyssal Scepter: REDUCES not penetrates MR by 20 this isnt really any different from penetration, because you cannot have more than one of the Auras applied. However with certain champions which have skills that reduce MR it is quite effective (for example Fiddle's Innate aura reduces their MR by 16 i think and this by 20 which mean they have lets say -6 MR this means you deal BONUS DAMAGE this does not stack with penetration, i think, and it is applied before Voidstaff's 40%)
If they are stacking a lot, grab Voidstaff, if not really grab sorc boots, which you should always have on zil