This point is raised a lot and people compare Canon 600D with Nikon D5100 based on not having focus motor but are unclear what is the impact of this ???
Here is a small comparison of relevant lenses (cheap ones only) that do not work with Nikon D5100 and D3100 in AF mode.
70-300mm f4-5.6
Nikon AF-S ~ $550
Nikon AF ~ $170 ----------- AF doesn't work
Canon version ~ $430
24mm f2.8
Nikon AF ~ $350 ------------ AF doesn't work
Canon version ~ $360
28mm f2.8
Nikon AF ~ $260 ------------ AF doesn't work
Canon version ~ $260
35mm f2
Nikon AF ~ $350 ----------- AF doesn't work
Canon version ~ $330
50mm f1.4
Nikon AF ~ $310 ------------- AF doesn't work
Canon version ~ $370
50mm f1.8
Nikon AF ~ $115 ------------- AF doesn't work
Canon version ~ $110
85mm f1.8
Nikon AF ~ $425 -------------- AF doesn't work
Canon version ~ $390
60mm f2.8 macro
Nikon AF ~ $500 -------------- AF doesn't work
Canon version ~ $450
There are AF-S versions of all above lenses in Nikon and some are with better apertures but very expensive.
Note: I have not included high-end lenses in this list.
I hope this comparison helps to decide whether 'not having focus motor' is important to you or not.
If u don't want above lenses then its a non-issue 
Update for Alternatives:
Fine. These lenses don't work then what choices are there which auto-focus ??
Here are some popular choices with reasonable prices:
- Nikon 18-55 AF-S (kit lens)
- Nikon 18-105mm AF-S ~ $370
- Nikon 55-200mm AF-S ~ $250
- Nikon 55-300mm AF-S ~ $400
- Nikon 70-300mm AF-S ~ $550
- Nikon 50mm f1.8 AF-S ~ $220
However, Canon has the advantage that above cheaper lenses work with all DSLRs and also have better versions available meaning much more choice for lenses.
