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Unlocks and bonuses can be obtained in the basement/bot room.
They unlock you new clothes, icons, bots, rooms, etc.
The best place to find out what the unlocks are is this site:
http://www.oocities.org/dmo_complete_unlocks/index.html
BUT... some of the information on there is wrong (And yes, I'm 99% sure:P)

This is a list of all the incorrect data:
Soothing Rain: Obtained by placing 3 'Solemn Wish's on the field.
Para/Dox Bot: Along with summoning the gate guardian, you must sacrifice a labyrinth wall with magical labyrinth attached to special summon wall shadow to unlock these bots.
Rebecca Bot: Along with summoning 3 mill shields, you must bring a shadow ghoul's attack up to 3000 to unlock this bot.
Bot Multi-Opp Room: Along with getting 80% or more bonuses, you need to have unlocked 'Tier 2 Bots' to get this floor.
I'm pretty sure there's a few more; I'll keep you guys posted!

Also, I guess you'd want to know what the tiers are? Presenting... a list of tier bots (Thanks Guzame!):

Tier 1: Yugi Muto, Téa Gardner, Tristan Taylor, Bakura Ryou, Solomon Muto
Tier 2: Rex Raptor, Espa Roba, Weevil Underwood, Bonz, Mako Tsunami
Tier 3: Mai Valentine, Bandith Keith, Joey Wheeler, Maximillion Pegasus
Tier 4: Arkana, Rare Hunter, Lumis and Umbra, Strings, Odion
Tier 5: Ishizu Ishtar, Marik Ishtar, Seto Kaiba, Shadi
Tier 6: Simon, Yami Bakura, Yami Marik Ishtar, Yami Yugi
Defeat all of those 5 times to unlock Dartz!