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First, the T61 came with the 7-cell battery, the T400 with the 9-cell. The batteries are 100% compatible to both laptops, but the 9-cell was only released late into the T61 life cycle, probably due to many customers with 14" wide models complaining that the 7-cell is not enough.
Here are the two batteries next to each other:
And the laptops with the batteries sticking out back. The 9-cell really sticks far and diagonally too. This was done to somehow keep the footprint of the laptop within reasonable bounds and also keep it compatible with the Advanced Dock. Still, with the 9-cell batteries these 14" widescreens are huge. Compared to a 14" 4:3 T60, they are wider (due to the widescreen), and just as deep, due to the battery sticking far far back. Design which is far from ideal, IMO.
Other that the battery, the chassis of the laptop is almost identical in shape, size and looks, but there are a few subtle differences. First, consider the right side and the optical drive (T400 above T61 here):
You can see, that while the T61 bezel is totally flat here (like on the T60), the T400 has the bottom of the bezel curved, similar to the T4x series. This makes the optical drive bezel curved as well. Because of the shape of the bezel, the front-to-back difference in thickness is less pronounced in the T400.
The optical drives, BTW, are incompatible, as T61 uses PATA drives (bottom), while T400 uses SATA (top):
Interestingly, although the asymmetry in the screen bezel is present in the T400 as in the T61, on the T400 they tried to improve the looks a little bit, by doing two things:
1) Placing the screen a bit higher inside the lid (so that the bezel is wider at the bottom and narrower at the top), as evident from the following pictures:
2) Making the antenna covers a bit narrower and changing the texture so it is less conspicuous and distracting, as can be seen from the pictures of the top bezel (T61 on the left, T400 on the right):
The palmrest is different too. First the touchpad. On the T400 (right), it is bigger and widescreen-shaped, which makes sense on a widescreen laptop. Also has nice scroll stripes.
Also, the fingerprint reader is a bit smaller on the T400 (right), and the logo is different. The T61 has the "T-series" logo, which is design this way to be compatible with the shape of the classic "IBM Thinkpad" logo. The logo itself is a sticker, and some T6x models came with the "IBM" logo, whereas others came with the "T-series" logo.
The T400, as all new Thinkpads sports the simple "Thinkpad" logo. Also on the bottom left of the lid (not pictured here), there is a "Lenovo" logo. I guess the transition of the brand is finally complete with these new Thinkpads.
This particular model of the T61 (bottom) comes with a card reader and a single PCMCIA slot, protected by a dummy card. The T400 (top) has ExpressCard/PCMCIA, protected by a spring door.
