There is no best format as such. Depends on use cases. Let us analyze yours
- Users will upload files from clients in various formats
- You want user clients to play files after downloading them
Optimization parameters would be
- Quality of audio
- Time take to download a file (size of files)
- Future efforts and device support
Quality of audio:
If you transcode properly with reasonable bitrate there isn't too much quality loss. That is the whole point of mp3/aac compression anyways. You can't tell the difference between 128Kbps AAC 44.1 KHz and a raw sample unless you had fantastic audio equipment in the first place and a good set of ears. So unless this is content production application don't worry too much. Ensure you give reasonable quality.
Size of files:
Wav files will be big compared to compressed content.
Future proofing and device support:
The most commonly supported audio formats are mp3 and aac. AAC is better than MP3. But you should get a good encoder for it (say nero). If your clients are PC's HE-AAC is a good choice. If it is mobile devices stick to AAC-LC. (no support for HE-aac in many of them)
In the future if you add streaming (I am guessing you will, it is the next logical step) the choice becomes more important. Not all devices support mp3 streaming. AAC streaming is more common.
Give all of the above I would say go for AAC.