Rod of many wands with eternal wands

[Vossler]

Ok wondering could u use and eternal wand or wands in a rod of many wands

[Rijan_Sai]

Ok wondering could u use and eternal wand or wands in a rod of many wands

Aside from Eternal Wands being classified as "Wondrous Items" rather than "Wands," I wouldn't see any reason why you couldn't, and from the DM perspective* I would allow it.... keeping in mind that EW's only have 2 charges per day. (AFB so I can't check the actually wording of the rod...)

*YMMV; this would have to fall entirely in the "ask you DM" side of things.

[Vaern]

Actually, the Eternal Wand isn't explicitly categorized as a wondrous item in the Magic Item Compendium. The section it is listed in is titled "Tool Descriptions," with the book's introduction stating "Tools" is a broad category that includes potions, scrolls, wands, and staffs in addition to wondrous items.
The Eternal Wand requires both Craft Wondrous Item and Craft Wand to create. It is at the same time a wondrous item and a wand, and I would argue that it could be used with a Rod of Many Wands as it is a wand by name, by feat requirement, and by description - being referred to as "a new form of wand." I don't think it would be difficult to convince your DM that an Eternal Wand may be used as a substitute for a classic wand for effects that require the use of a wand.

Bear in mind, though, that the Rod of Many Wands drains a number of charges from each wand equal to the number of wands inserted into it. As an Eternal Wand only functions twice per day as printed, you will be unable to use three wands with the rod if one or more of those wands is Eternal (unless you do some customization and repricing to make the wand function at least three times per day).