We would like to spend 3 or 4 days in Lisbon the latter part of September. Any suggestions re accommodation that is reasonable and clean in the city centre?

I visited Lisbon last year and loved the city. I rented an apartment that was really clean and located in a nice building, friendly neighbors. It was also in a central location that I felt safe walking back home at night alone.
http://www.homeaway.com/vacation-ren...?uni_id=147869

Owner is really nice and was prompt with answering any questions I had. Plus it was a major plus since the airport bus dropped you right near the apartment.

Define reasonable.

Reasonable I would think around 80 Eur a night.

OK, this place would work at the right time of year - http://www.residencialflorescente.co...hp?lg=eng&op=0 The other place I've stayed at is rather more and not, in my view, worth the money. Florescente is very well located, although a bit bare bones. Ask for a room on a higher floor or you may be looking right at the breakfast room. (Click on my name for my Lisbon TR.) I hear good things about a youth hostel called "The Traveler's House" ...

We are staying in a couple of weeks in Baixa at Brown's Luxury Apartments. It is really a studio and rather large.
We are paying E90 a night but that is considered a high season price because it is August.
It is really a 300m bedroom with bath and kitchenette. I really do not know how it is because we haven't stayed there yet. It looks very high end but of course no breakfast as it is an apartment.
You can check it out on www.rent4days.com
Good luck.