Depending on your exact code, different branch instructions are your friend.
Here
if(memory[pointer] > 0) goto IL_0002;
in IL:
IL_001f: ldsfld uint8[] BFHelloWorldCSharp.Program::memory
IL_0024: ldsfld int16 BFHelloWorldCSharp.Program::pointer
IL_0029: ldelem.u1
IL_002a: ldc.i4.0
IL_002b: bgt IL_0002
Basically, you push the values you want to compare onto the stack, and then call bgt to go where you need to.
OpCodes Class IL, brtrue/brfalse beq.
if #, ILDASM Reflector IL.