I've worked and trained both 61 and 141...
61 is usually better, but you will need to find a good, well-managed small school, or be prepared to aggressively manage your own training in the FBO environment. This will save you money.
141 has an inherent structure, but they usually use that as an excuse to charge more, especially since ex-military folks using the VA can afford it. Also the 141 structure is NOT flexible...unlike 61, you cannot focus your training where it's needed. You will end up wasting money repeating things you have already mastered because the syllabus says so, but if you need more work on some other skill you will pay out-of-pocket for training in excess of the syllabus.
141 advocates (and salesmen!) always brag about how 141 requires fewer flight hours for each rating. This is true, however...they usually charge enough that you end up paying about as much as you would for 61 training. Of course you grduate with fewer flight hours, which is a good thing, right?
WRONG! In case you hadn't noticed yet, pilots get hired based on experience, which means flight time! It's silly to pay more for less flight time. The ONLY things that matter in aviation are FAA certificates, flight hours (in REAL airplanes, not simulators), and who you know. The school you went to or the type of training is meaningless unless it is military.
Unless you are a VA student, I would not consider 141 unless you have a really good reason to do so, or you can independently verify that the school is a good one.