Is there a benefit to harvesting my garden?

Question

I've unlocked the garden in cookie clicker. There is a counter for the number of (mature) plants harvested. Other than Bakeberry, why would I harvest plants?

Answer 1

As stated in this wikia article:

In the Garden, plants and fungi can be grown and crossbred, obtaining new species as a result. Crops provide various benefits depending on the species, some granting passive buffs as they sit planted in the Garden, while others give rewards when harvested.

There is also another document with much more information concerning Garden and what it is used for, here. Author claims to have read this information direclty in the source code. You will find there:

• Recipes for plant mutations
• Plant mutation mechanics
• Efficient plant arrangements for breeding
• Soil Type Data
• Plant Effects
• Garden Tools
• Garden Related Achievements
• Garden related upgrades

Additional information related to plants can be found on this link.

Reading your question again, I will describe Plant Effects, as it is I think the correct answer to your question.

Plant Effects

• Baker's Wheat: +1% CpS
• Thumbcorn: +2% cookikes per click
• Cronerice: +3% grandma CpS
• Gildmillet: +1% golden cookie gains, +0.1% golden cookie effect duration
• Clover: +1% golden cookie frequency
• Golden Clover: +3% golden cookie frequency
• Shimmerlily: +1% golden cookie frequency, +1% golden cookie gains, +1% item drops
• Elderwort: +1% wrath cookie gains, +1% wrath cookie gains, +1% grandma CpS, Immortal (immune to contamination and decay), surrounding plants (3x3) age 3% faster
• Bakeberry: +1% CpS, Harvest when mature for +30 minutes of CpS (capped at 3% of bank)
• Chocoroot: +1% CpS, Harvest when mature for +3 minutes of CpS (capped at 3% of bank) predictable growth
• White Chocoroot:
  +1% golden cookie gains, Harvest when mature for +3 minutes of CpS (caped at 3% of bank) predictable growth
• White Mildew: +1% CpS, may spread as brown mold
• Brown Mold: -1% CpS, may spread as white mildew
• Meddleweed: useless, may overtake nearby plants, Sometimes drops Brown Mold or Crumbspore when uprooted
• Whiskerbloom:
  +0.2% milk effects
• Chimerose: +1% reindeer gains, +1% reindeer frequency
• Nursetulip: Surrounding plants (3x3) are 20% more efficient, -2% cps
• Drowsyfern: +3% CpS, -5% cookies per click, -10% golden cookie frequency
• Wardlichen: 2% less wrath cookies, wrinklers spawn 15% slower
• Keenmoss: +3% item drops
• Queenbeet: +0.3% golden cookie effect duration, -2% CpS, harvest when mature for +1 hour of CpS (max. 6% of bank)
• Juicy Queenbeet: -10% CpS, surrounding plants (3x3) are 20% less efficient, harvest when mature for a sugar lump
• Duketater: harvest when mature for +2 hours of CpS (max. 8% of bank)
• Crumbspore: explodes into up to 1 minute of CpS at the end of its life cycle (max. 1% of bank), may overtake nearby plants (contamination)
• Doughshroom: explodes into up to 5 minutes of CpS at the end of its life cycle (max. 3% of bank), may overtake nearby plants
• Glovemorel: +4% cookies per click, +1% cursor CpS, -1% CpS
• Cheapcap: buildings and upgrades are 0.2% cheaper
• Fool’s bolete: +2% golden cookie frequency, -5% golden cookie gains, -2% golden cookie duration, -2% golden cookie effect duration
• Wrinklegill: wrinklers spawn 2% faster, wrinklers eat 1% more
• Green rot: +0.5% golden cookie duration, +1% golden cookie frequency, +1% item drops
• Shriekbulb: -2% CpS, surrounding plants (3x3) are 5% less efficient
• Tidygrass: surrounding tiles (5x5) develop no weeds or fungus
• Everdaisy: surrounding tiles (3x3) develop no weeds or fungus, immortal
• Ichorpuff: surrounding plants (3x3) ages half as fast, surrounding plants (3x3) are half as efficient