Choosing an S3 backup client is just like choosing any other backup program. You should make sure you get a cross-platform client, for example, so you can restore files anywhere and at any time. Although there's strictly no need to encrypt data stored in S3 (data in a bucket is private unless you deliberately make it public), most clients will also encrypt it. That can create problems. Although clients normally use standard forms of encryption, such as AES, the specific method of encryption will probably tie you into using that particular client when it comes to restoring files. Don't assume you can simply dip into your bucket manually to grab files.
How cheap is S3? With S3 you pay for transfer in and out, as well as the storage space your files take up, although the individual fees are very small.
The initial transfer of around 50GB of files will cost about $5, for example, at 10 cents transfer fee for each gigabyte uploaded. Every month the charges will be 9.3 cents of "rent" per gigabyte, making $4.65 in total, although if you upload a further gigabyte or two each month you'll be looking more at a total of around $5 per month. Assuming a growth of 2GB per month in terms of new files you decide to backup, a year later you'll be paying around $8 per month for 74GB of storage--still pretty good value.
If using an S3 backup client sounds like too much hassle, you could use one of the many FTP clients that support S3, and manually copy files to your S3 space when required. Again, you'll need to use your public and private key as your username and password, but aside from this there's no difference between using S3 and an FTP site. Files won't be encrypted but, as mentioned, S3 is technically secure (although hackers gaining access in some as-yet unknown way will always be an issue). You could also use something like TrueCrypt, a cross-platform and open encryption package, to encrypt any particularly sensitive data before uploading it.