In the Expanded Universe, the Wookiees shifted back and fourth quite a bit between Separatist and Republic. During HoloNet News, it seemed as though the Wookiees would side with the Separatists against the Republic, but by the time of ROTS, we see the Wookiees fight against invading battle droids. What happened in between? Since I tried to sort out the post-ROTJ events on Kashyyyk a while back, I thought I'd take a shot at the pre-ROTS sources:

Wookiee relations with the Trade Federation have never been the best. A decade before the Clone Wars broke out, the Trade Federation contested Wookiee colonization rights to Alaris Prime, a moon of Kashyyyk. Wookiee colonists on the moon fought several skirmishes against battle droids and Trandoshan slavers, with whom the Federation had allied itself. Jedi Obi-Wan and Qui-Gon aided the Wookiees in driving the Federation from the moon. (Galactic Battlegrounds) Many of the Wookiee colony worlds also repelled encroachments by the Trade Federation. (Incredible Cross-Sections: ROTS) Kashyyyk itself came under attack by brand new Federation "super" battle droids, led in secret by Count Dooku. (Battlefront) Master Yoda visited Kashyyyk around this time, possibly in response to this attack. (Jedi Quest)

It appears that their alliance with the Federation emboldened the Trandoshans, who petitioned the Senate for equal senatorial representation. Kashyyyk nearly joined the Separatists over the issue, and Oppo Rancisis attempted to mediate between the Trandoshans and the Wookiees. When the Clone Wars began, Kashyyyk still wavered between Separatist and Republic camps.(HoloNet News)

The Alaris Prime colony, however, remained loyal to the Republic, designing and producing the Decimator weapon. It came under attack twice by the Confederacy during the early months of the war. (Clone Campaigns, The Clone Wars) The Kashyyyk government viewed these battles as a colonial matter that did not involve Kashyyyk itself. (HoloNet News)

After continued diplomacy from Yoda and Kai Justiss, the Wookiee Senator Yaura rejected the Confederacy's open invitation and sided with the Republic. (HoloNet News) In response, the Trade Federation courted the Kashyyyk Royal Families (who were not yet ready to commit to the war) directly, hoping to win their support. An impatient General Grevious ordered a small invasion force sent to Kashyyyk. The droid army killed the son of King Grakchawwaa, leading the Royal Families to join Senator Yaura in support of the Republic. (Visionaries: Deep Forest) This force was the first of many Confederacy incursions to bypass the colonies and invade Kashyyyk itself. (ICS: ROTS, Databank)

With the Wookiees now dead set against the Separatists, the Federation found eager supporters in its old allies, the Trandoshans. A Trandoshan invasion of Kashyyyk resulted in the capture of General Tarfful (Republic Commando) and was quickly followed by Separatist forces. (Clone Wars) Kashyyyk needed help, which came in the form of General Yoda... (Revenge of the Sith)