The best choice of garden amendments depends on the current soil and which varieties are planted in it.
Gypsum and lime are both useful soil amendments for gardens. However, neither should be used without a soil test to determine whether they're needed at all, as well as which one meets your gardening needs and in what quantity. The usefulness of either soil amendment is largely determined by what plants will be used in the garden.
Gypsum Benefits
Gypsum is calcium sulfate. It provides garden soil and the plants grown there with calcium and sulfur, and both are necessary for plant growth. Gypsum does not change soil pH, meaning it can be used on soils where the pH is already balanced properly for the plants that are growing there. Gypsum also helps relieve plants plagued by salty soils, since it reacts with the salt, changes its structure and allows it to leach away. Given enough time, gypsum can improve the drainage problems inherent in heavy clay soils.
Lime Benefits
Lime sold as a garden amendment is either calcium carbonate or calcium magnesium carbonate. Both are alkaline materials and will help neutralize soils that are too acidic for the plants that will be grown there. Both have high amounts of calcium, which plants need for structure. Calcium magnesium carbonate, or dolomite lime, also contains another important plant nutrient, magnesium.
Gypsum Drawbacks
Gypsum won't help rectify acidic soils. It also is not as useful in amending poorly drained soils as compost is. Neither will gypsum work in poorly drained silt or sand soils.
Lime Drawbacks
Using lime in alkaline or neutral soils throws off the pH balance of the garden soil, making it inhospitable to many plants. Some plants also respond poorly to excess magnesium in the soil, meaning that applying dolomite lime when the soil already has sufficient or excess magnesium is harmful to garden plants. Lime does not correct poorly drained soils.
Considerations
If a soil test reveals that the soil is too acidic for the plants that grow there, with poor calcium and little nutrition, lime is the best choice for that garden. If a soil test reveals that the soil is heavy clay, has a neutral or alkaline pH, has poor calcium and perhaps even has excess salts, gypsum is the better choice.
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