ModTweaker is an addon for MineTweaker 3. Minetweaker lets you adjust recipes, remove them entirely, or add new recipes. While it has decent mod support, there are many mods that use custom crafting handlers that are not supported natively. ModTweaker plans to provide additional support for as many of these mods over time as possible.

Stable Releases on Curse

http://minecraft.curseforge.com/mc-mods/220954-modtweaker

Development build on jenkins

http://ci.tterrag.com/job/ModTweaker2

Guidelines for Bugreporting

https://github.com/jaredlll08/ModTweaker2/wiki/Bug-Reporting-Guidelines

Supported Mods

Applied Energistics 2
Auracascade
Botania
Chisel
ExNihilo
ExtendedWorkbench
Factorization (0.8.95+)
Forestry (3.6.0+)
Flaxbeard's Steam Power
Mariculture
Mekanism 8
Metallurgy
PneumaticCraft
Railcraft
Tinkers Construct
Terrafirmacraft
Thaumcraft
Thermal Expansion